When David and Amy first go through the tunnel and end up in the office, David is holding the flashlight in his hand when he pushes up on the door. The camera angle changes to inside the office and his hand is empty.
When David peeks out of the tunnel in Mason's video room, he pushes the latch up with the flashlight in his right hand. In the next shot from outside of the tunnel, the flashlight is not in his hand anymore.
The apple from which Amy was cutting a slice in the car in the beginning of the movie is later discovered "planted" by the bathroom sink after the first blackout. At least 2 or 3 hours have passed between when Amy cut the apple and when she finds it by the sink in the room, but the apple hasn't browned at all during this time, when it reality it would have browned within minutes of being cut.