The Beast Below:

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Notice that there's also a Smiler booth just about visible in the corner which wasn't there a moment ago!
In the pre-credits scene, as young Timmy stands outside the lift doors, the wide shot shows the wall at the end of the corridor having a large window that looks out to space. But as the lift doors open and we cut to a close-up, now the end of the corridor looks completely different — the window has vanished, replaced by a drab grey wall.

20 As Timmy gets into the lift, the Smiler inside is clearly showing its happy face. But in the next wide shot, the Smiler is showing its "frown" face. Furthermore, the next time we see the Smiler, it's back to its smiley face again (and only then starts to turn to a frown). A similar thing happens a moment later when the lift floor opens up: the wide shot shows the Smiler's angry face, but then we see a close up and it's back to "frowning" again (and only then starts to change to its angry face).

30 Speaking of the Smilers and their angry face, stop and ask yourself how the Smilers' heads could rotate 180 degrees three times, showing a different face each time?
[It's like having a coin with three sides!]

40 In the first shot of Amy floating in space outside the TARDIS, the Doctor is holding Amy's calf, with his fingers at the back of her leg. In the next close-up, the Doctor has his hand around her ankle instead, with his fingers at the front.

50 In London Market, when the Doctor uses a glass of water to check the vibration of the engines, two distinctive extras dressed as businessmen walk past behind him. A few seconds later, the same two extras walk past again!

60 When Amy wakes up in the voting booth and the computer verifies her identity, the screen displays her age as 1,308 — but the computer voiceover says "Age: Thirteen hundred and six".
[Maybe this mistake was a deliberate distraction so we don't think about why Amy Pond is still listed on the UK electoral register over a thousand years after her death!]

70 After pressing the "Forget" button in the voting booth, Amy sees a video message of herself, begging her to get the Doctor off the ship. (The implication is that Amy recorded the message right before pressing the "Forget" button.) In the message, her mascara has run and her eyes are puffy, apparently from crying. Whereas in the "live" shot, Amy's eyes are still tearful but no mascara streaks can be seen. Then a moment later, when the Doctor steps into the booth and asks Amy what she's done, we see a close up of Ms. Pond's eyes and they're bone dry — no sign that she'd just been crying.

80 When the Doctor and Amy end up in the whale's mouth and the Doctor reveals that they're standing on a giant tongue, keep a close eye on the Doctor's feet — there are a few moments when the surface of the "tongue" looks suspiciously like a sheet of cloth, due to the way it stretches as the Doctor walks around on it.
[Admittedly, I've never met a real Space Whale — maybe their tongues really are made of cloth?]

90 And just a moment later, as the Doctor comments that "the normal entrance is closed for business", it's revealed that the Doctor and Amy have been standing less than ten feet away from the whale's giant teeth. Why didn't they notice these massive gnashers the instant they landed in the mouth?
[Yes, the Doctor had only just started using the sonic screwdriver as a torch, but most of the lighting seems to be coming from elsewhere]

100 Although both the Doctor and Amy are soaking wet and covered in chunks of whale vomit after being ejected from the whale's mouth, only a couple of scenes later as they enter the Tower, while Amy has the good sense to still look somewhat bedraggled, the Doctor's outfit looks bone dry and spotless!

110 The "Tower of London" is supposedly a dungeon in the deepest bowels of Starship UK, and yet there are multiple (blacked-out) windows clearly visible in the background.
[Presumably the actual windows of Neath Abbey in Wales, where the scene was filmed]

120 When our heroes first enter the Tower, we get a good look at the "pit" containing the tentacles and the metal grid that covers it. A couple of minutes later, when the Doctor releases the tentacles from the pit, he bends over as if to lift the grating and throw it out of the way. Although we hear a suitably metallic sound effect, notice that Matt Smith isn't actually holding anything in his hands!
[Somebody forgot to add a special effect...]

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The differing surroundings of both flags means these shots are clearly meant to be opposite sides of the ship. That still doesn't explain why one flag is upside-down though!
At both the beginning and end of the episode, we see a long shot of Starship UK, with a large Union Jack on the side. Unfortunately, in the shot at the end of the episode, the flag is upside-down!
[Compare the position of St Patrick's Cross, i.e. the red diagonal stripes]

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