In Amy's lab there is a dark green compressed gas cylinder with a "Flammable" label. Dark green is used for inert gases that are not flammable.
When Leonard was racing his horse on the XBox using Kinect, he was whipping his horse with his left hand while his jockey avatar in the game was using his right hand.
Amy keeps asking if the girls menses have synced up. The notion that this happens is a myth and as a biologist, Amy would know that.
When Sheldon is in Amy's apartment to comfort her, several books can be seen on a table behind the couch. They are lined up with their spines (and titles) facing away from the couch. Their location was clearly designed to be convenient to read on the couch, yet the titles cannot be read to identify any book from the couch. This issue would become immediately apparent the first time Amy tried to read one.