The Eleventh Hour -
While hanging from the TARDIS, the Doctor looks up into it and for a couple of seconds has a confused look on his face.
When Rory and Amy exit the elevator on the second floor of the hospital, Rory glances behind him at something, but when he looks back towards Amy, he shakes his head like he forgot something. It is about 42:49.
In the scene at the end of the episode where Amy goes into the TARDIS for the first time. there’s one point where she leans back on the console and is looking around the room. The camera is pointed towards her face, so we can’t see what she’s looking at. She looks around with a sort of awe-struck smile, but then her eyes linger over something and her expression turns into a look of horror. She starts breathing really quickly and turns as if to get the Doctor’s attention, but as soon as she’s facing him she just asks, perfectly normally, “Why me?”, as if she’d completely forgotten about what she’d just seen. Also, she flicks a TARDIS button/switch/lever at this point. Accidental Amy or something meaningful?
The Beast Below - At around 9:25 a black figure walks past Amy, she looks confused/scared for a couple of seconds then shrugs it off.
Victory of the Daleks - Near the end after the Daleks escape, the Doctor moves slowly backwards, as he gets near to the green framed window/doorway he looks to his left with a shock. The camera then switches to Amy and Churchill who both stare to the Doctor’s left with a look of shock before Amy continues on as normal with the line “Doctor, it’s OK you did it, you stopped the bomb.”
The Lodger - At 21:47 for a couple of shots Amy looks in the distance or at the screen and gasps, then shouts for the Doctor’s attention but he doesn’t listen. She looks away and shakes it off.
Vampires of Venice - At the end when Rory, Amy, and the Doctor are standing by the TARDIS, the TARDIS door is open and then shuts on it’s own.
The Big Bang - There are cloaked figures behind the Sarcophagi in the museum; a third figure moves out of shot at the edge of the screen at about 13:31
So I watched these all, and… dear gog i’m scared. Especially in “The Big Bang”. There are definitely cloaked figures behind the Sarcophagi aaaaaaa