Plot hole: After Professor X crashes his mini-jet onto the hospital roof and loses consciousness, he isn't discovered until Jean mentally locates him. An aircraft crashing on the roof would cause enough noise to immediately alert staff and anyone else in the hospital of his predicament.
00:09:15 - 00:15:45
Plot hole: Wolverine's enhanced sense of smell should have alerted him to Erik the Red's spy on the roof. Failing that, the video feed Erik the Red is receiving from the spy shows Wolverine, Beast and Professor X looking right in the spy's direction, so they would have seen him.