Audio problem: Adam throws a very small object at the mirror with his second throw. Yet the sound is of something a lot bigger hitting the glass. (00:29:35)
Audio problem: When Dr. Gordon is dialing 911, we hear one low tone then two higher tones. On touch-tones phones, 1, 4, and 7 are the lowest tones while 3, 6 and 9 are the highest. Gordon would have dialed a 1, 4 or 7 first and then a 3, 6 or 9 twice in succession. Possibly 1-9-9 for Emergency? (00:55:50)
Audio problem: When Dr Gordon is cutting off his foot, the screams from Adam are just a replay of the screams he does at the end of the film. (01:27:05)
Audio problem: When Larry goes out into the hall after seeing to his daughter, Ally starts to talk to him but her mouth doesn't move with the words.
Chosen answer: Yes. You pretty much guessed correctly. We can assume that Jigsaw told Zep to tell Ali to tell Dr Gordon, "do not believe Adam's lies..." Don't forget that Jigsaw spends hours planning his tests so it would be safe to say that he had planned it all in the beginning.