The Eleventh Hour:

10 During the pre-credits sequence, as the new Doctor hangs out of the TARDIS by his fingertips — keep an eye on the floor just inside the TARDIS doorway: half the time, the edge of the floor has a raised ledge/lip and half the time it doesn't.

20 Also, in the close-ups of Matt Smith dangling out of the door, watch the background to notice that the TARDIS passes over the distinctive pyramid-topped Canary Wharf tower twice in rapid succession, with seemingly no time for the TARDIS to turn around and go in the opposite direction between the two shots.
[I could also pick on the fact that you can clearly see the Millennium Dome in the background, which wasn't built until 1999 — when this scene is "meant" to be set in 1996 (i.e. twelve years before 2008 — see below). However they never explicitly state the year in the script, so I'll let them off]

25 Another inconsistency in the pre-credits scene is the St. John Ambulance badge on the right-hand TARDIS door. The physical door deliberately has no badge on it until the end of the episode, after the Doctor mentions his "brand new TARDIS". However, in some of the CGI in the opening scene (for example, right after the Doctor's close encounter with Big Ben), you can prematurely see the badge on the TARDIS door — which then disappears in other CGI shots during the same scene.

30 Throughout the entire pre-credits scene, observe Matt Smith's amazing colour-changing shirt: in the CGI long shots, his shirt looks white, whereas the close-ups clearly show the shirt as being a light blue. Then as he climbs into the TARDIS, it instantly changes shade of blue between cuts, due to differing lighting.

40 When the TARDIS crash-lands, young Amelia leaves her house to investigate. As she walks through the garden, the TARDIS window lights are clearly off — but a few seconds later as she gets to the TARDIS, the lights are now on.
[Mind you, the TARDIS did just crash. A power fluctuation perhaps?]

50 When the Doctor bangs his head against the tree in Amelia's garden and falls to the ground, his hair looks noticeably drier and neater than it was a few seconds before (especially around the forehead).

60 The apple Amelia gives the Doctor starts out as red, then becomes a green apple almost immediately after he takes a bite and spits it out. A moment later, the bitten apple can be seen in the fruit bowl on Amelia's table — with no indication that Amelia had turned around to put it there — and the apple is now red again! Finally, as Amelia returns from the fridge carrying a yoghurt, the apple has disappeared from the fruit bowl entirely.

70 After downing the yoghurt and wiping his mouth, the Doctor still clearly has a smear of yoghurt left on his chin, but in the next shot it instantly vanishes.

80 When the Doctor drinks from the big bowl of custard, he appears to finish most of it. However, a few seconds later, after he puts the bowl back on the table, it still seems to be half-full — and furthermore, the top of the bowl has no "tide mark" on the side from which he supposedly just drank.

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I'm trying to *picture* how this could have happened, but so far I'm *drawing* a blank... (see what I did there?)
As the Doctor investigates Amelia's room, we see the side of her wardrobe, which has some of her drawings taped to it. Before the crack opens, keep an eye on the two drawings in the middle, directly above the panda drawing. When the crack opens, those two drawings disappear completely! They magically reappear again after the crack closes.

100 As young Amelia watches the Doctor leave for "5 minutes", in close-up her hair gets wildly blown around by the dematerialising TARDIS, but in the next shot (from behind), her hair is instantly motionless.

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So basically it's the opposite of that song "Don't it Make my Brown Eyes Blue"?
Young Amelia has blue eyes, whereas grown-up Amy has light brown eyes.

115 The Doctor is handcuffed to the radiator on the first floor landing of Amy's house (that's "second floor" if you're American) and we see a flight of stairs beside him leading upwards, i.e. it must be at least a three-storey house. But the outside view of the house clearly shows it as two-storey (with no sign of an attic conversion).

120 When Amy enters the hidden room and the creature reveals itself, the Doctor instantly knows it's an "interdimensional multiform" — but how can he possibly know this? He's handcuffed to the radiator down the hall and can't see or hear it, and he hasn't been anywhere near the room. All he has to go on is that it has a perception filter at its disposal.

130 Since the "hidden" door hasn't been noticed in a least a dozen years, how come the paint isn't any worse off than the paint on the other doors on the landing?

140 When the Doctor first meets adult Amy, he asks how long ago Amelia Pond stopped living at the house, to which she replies "6 months". But a while later, when he realises the garden shed is 12 years old (i.e. it's been 12 years since his last visit), he repeatedly asks her "why did you say 6 months??" Why does that matter? Who says Amelia moving out and the age of the shed (i.e. the timing of his last visit) have anything to do with each other?

150 When the Atraxi start their broadcast, Prisoner Zero is standing on the first floor landing of Amy's house. He then walks into a side room to the right of the "secret door" and looks out of the window. (Note the distinctive patch of peeling paint on both the window ledge and the adjacent wall.)

From the preceding shot, you'd have to conclude that this window is clearly at the side of the house. However, a few minutes later as the Doctor and Amy are in the garden at the rear of the house trying to open the TARDIS, we see Prisoner Zero at this same window growling at our heroes, with a corresponding reaction shot from Amy — implying that they can see each other, even though they shouldn't be able to! (i.e. Prisoner Zero is at the side of the house and Amy is out back.)

Just to confirm that this is a blooper, near the end of the episode when Amy and Rory run into the back garden as the TARDIS disappears, you can see that the window with the distinctive missing paint is in fact the upper middle window at the rear of the house — in other words, the window right behind where the Doctor was handcuffed! (Not some side room off the landing after all)

160 As the Doctor and Amy walk along the street in Leadworth, keep an eye on the lady riding a mobility scooter in the background. As the Doctor says "I've got a post office, and it's shut" she can be seen making a turn to her left. But in the next shot, she magically jumps back to the direction she was originally travelling in.

170 A moment later while walking along the same street, Amy and the Doctor walk past a red Mini Cooper (with white stripes) parked near the duckpond. A few minutes later, when Rory and Amy need to drive to the hospital, it turns out that this is Rory's car, but instead of being beside the duckpond, it's now parked at a different part of the village green, outside a white building that appears to be a bookshop.
[Yes, it's technically possible there are two identical models of that very distinctive car in a small village — but highly unlikely!]

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And look at the difference in his hair! Whoever did the continuity for this episode should have been the one slapped on the head...
When the Doctor slaps himself on the forehead while standing by the duck pond, observe that Matt Smith must really have hit himself quite hard, because his forehead is visibly reddened. But when he turns around and the camera zooms in on his eye, the redness instantly disappears.

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Besides, why doesn't she step outside for a better look, instead of trying to peer through the tiny, grimy windows of a phone box?
When we see the residents of Leadworth filming the sky with their cameraphones, one woman is shown filming from inside a telephone box. Leaving aside the question of why someone with a mobile phone is using a phone box (maybe she was out of credit), notice that she's supposedly filming the Atraxi ship blocking out the sun, but she's holding the phone way too low, basically pointing at the village church instead. (If you freeze-frame, you can even briefly see her screen and sure enough, it doesn't show the Atraxi ship!)

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To be honest, haven't we all done this at one time or another - accidentally taken a selfie instead of a photo?
During the same scene, when we look over Rory's shoulder as he's supposedly filming Prisoner Zero on his phone, his screen just shows a reflection of Arthur Darvill's own face!

210 Rory's hospital badge says "Issued 30/11/1990". Considering everyone is using camera phones and Wi-Fi, this episode is clearly meant to be set in 2008 at the earliest. There's no way Rory is old enough to have been a nurse for 18+ years! (i.e. in his late 30s at least)
[And in case you think that he's just way older than he looks, it's clearly stated that he grew up with Amy]

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What time is it? Time to fix your watch, Amy...
When Amy catches the "smiley apple" thrown by the Doctor, notice that she's wearing her watch inside out! (i.e. with the back of the watch facing outwards)

230 Barney (the coma patient with the dog) is unshaven when we first see him in the hospital. Then a short while later, when Doctor Ramsden orders Rory to take some time off work, Barney is visibly clean-shaven. OK, a nurse could have shaved him in the meantime, that's not impossible... but only a few minutes later when we next see Barney (after Prisoner Zero escapes through the drain) he's unshaven again!
[Is extra-fast stubble growth a side-effect of being possessed by Prisoner Zero? If so, Barney would look like a member of ZZ Top by the end of the episode!]

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Yes, obviously it looks this way because it was a prop. Were there really no actual storm drains in the location they used?
When our heroes inspect the drain that Prisoner Zero escaped into, notice how poorly-designed it is: the grating is actually flush with the top of the kerb rather than being at road level. In other words, water on the road would have to flow upwards in order to drain away...!

250 The Doctor mentions Fermat's Last Theorem and its famous missing proof, saying that "Poor old Fermat died in a duel before he could write it down". Erm, no — Fermat claimed to have found his proof in 1637 and lived for another 28 years afterwards: more than enough time to have written it down! Moffat seems to be confusing him with fellow French mathematician √Čvariste Galois, who famously did die in a duel aged 20.

260 In the hospital, when Prisoner Zero takes the form of the mother and two daughters, the taller/longer-haired girl always appears to the left of the mother. When the Doctor crashes the fire engine's ladder through the window and Prisoner Zero turns to look, the two girls have instantly switched places. (To be precise, the picture has been flipped — the ribbons on the girls' heads give this away)

270 According to the clock in the hospital, it's 11.46am when Prisoner Zero breaks into the coma ward, but a couple of minutes later during "the word is zero" montage, we see shots of the New York Stock Exchange. It would be around 6.50am in New York, far too early for the NYSE to be open.
[Not to mention: one of the brief shots in the montage appears to be Piccadilly Circus — at night!]

280 Speaking of the hospital clock, it's clearly an old-school analogue "flip clock", which looks like it's been hanging in that ward for decades. Stop and ask yourself how a computer virus could possibly affect an old-fashioned non-computerised clock like that...?!

290 When Prisoner Zero transforms into "the-Doctor-and-Amelia" in the hospital, you can see right behind the Doctor's back as young Amelia starts speaking, and there's clearly nobody there. Cut to another angle and young Amelia steps out, supposedly having just been hiding behind the Doctor.

300 On the roof of the hospital, our heroes are looking up at the Atraxi ship in the sky when the eyeball "zooms in" on the Doctor. For a couple of seconds, Amy & Rory weirdly still keep looking up at the sky, and only then simultaneously look down as they seemingly just that moment notice the giant eyeball that's been right in front of them. How could they have missed it??

310 When the Atraxi eyeball starts scanning the Doctor, the camera from behind shows his head tilted to the left and the Atraxi's scanner beam pointing down towards his legs. The shot cuts to the front, and the Doctor's head is now upright, with the scanner beam shining in his face.

320 When the Doctor asks "is this world a threat?" and the Atraxi start reviewing historical footage, keep an eye on the Doctor as he stands on the left side of shot. The footage of Matt Smith has clearly been reversed and looped in order to prolong the length of the shot!

330 Also notice that just before the Doctor asks "is this world a threat?" he has a yellow patterned tie hanging around his neck, which disappears in the long shot, then reappears again in the next close-up.

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Does the "five second rule" apply to jackets too?
As the Atraxi review the various incarnations of the Doctor, Rory is standing behind him holding a selection of jackets. After the Doc says "Hello, I'm the Doctor", we can clearly see a distinctive burgundy-coloured jacket on the ground behind Rory to his right (our left). Cut to a close-up — and Rory is instantly holding the burgundy jacket in his arms.

350 After the Doctor tells the Atraxi to "run", their crystalline/snowflake ship begins spinning clockwise when viewed from below, but in the next shot as it makes its retreat, it's spinning anti-clockwise instead.

360 As the Atraxi spaceship flies away, the Doctor can be seen reaching into his left inside jacket pocket for the TARDIS key — then we cut to a close-up where he's merely standing watching the ship go, and only then starts reaching into his pocket (again).

370 In the final TARDIS scene, Matt Smith's hair is parted on his left (our right) as it has been for the rest of the episode, but just after he receives his new sonic screwdriver, one of the shots has clearly been "flipped" as his parting temporarily switches to the opposite side of his head.

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In fact, the Doctor starts wearing this patterned jacket two episodes later in Victory of the Daleks, so clearly this shot was filmed later on!
In the same scene, keep an eye on the Doctor's jacket: in the close-ups of him using the typewriter, the sleeves of his tweed jacket are noticeably lighter and have suddenly developed a checked pattern.

390 Why does Amy so readily believe the Doctor will have her back in time for her wedding the next morning, when he's just missed two appointments with her — by years?
[Mind you, would any of us turn down the chance to travel in the TARDIS, wedding or no wedding??]

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