When Rory, Ambrose, and Tony arrive in the Silurians' court, after the Doctor asks what happened to Alaya, the camera cuts to Ambrose, standing with her head over Elliot's right shoulder. When the camera cuts back to her, she's now standing with her head over his left shoulder instead.
(Around 31 minutes) as they are running from the Silurians the position of the sonic screwdriver varies from upright in the frontal shots to pointing horizontally in the over the shoulder shots.
According to The Doctor in "Flesh and Stone", Amy can remember the clerics and the Weeping Angels who fall into the space/time crack because she's a time traveler. Yet in this episode she forgets Rory after he's absorbed by the crack, which is explained as Rory was from Amy's personal life and the Clerics and Angels weren't. The Doctor explained this as he tried to keep Rory in Amy's mind, trying to help her remember him.
The Silurians refer to the humans and the Doctor as apes. However, the Silurians last lived on the surface during the Mesozoic, long before primates had evolved the Hominidae family (great apes). Apes started emerging about 40 million years after the end of the Mesozoic.
The Doctor has a respiratory bypass system so he shouldn't have been knocked out by the Silurian's gas gun.