Revealing mistake: When Benji imagines putting on a mask of an agent he plans to impersonate, when the camera pans around to first show the mirror, the mirror Benji's hands are further up on his face than the reflection, and the mirror Benji's hands move down his face slightly before the reflection starts to move them. Also, the mole that Ethan has on his left cheek isn't reversed in the mirror image. The "mirror" was actually a hole in the wall between two identical sets (one mirrored), with Simon Pegg and a Tom Cruise double in the foreground, and the mask actor and Tom Cruise in the background "mirror" set.
Plot hole: When Ethan and Benji go to Morocco, no one would know what the security card would look like or how it's programmed for them to make a copy to fit Benji's profile. Also issues with acquiring the BMW used to jam the signal at the gates, as the car is supplied by the IMF, which Ethan is no longer a part of, and Benji couldn't ask for it, as that would open him up to too many questions.
Plot hole: Before the IMF team can exchange the yellow cards for the access control, they first need to know the data format/file type in which the access rights (retina, gait, fingerprints...) are stored. Otherwise, the computer will not recognize the data on the card, and display an error to the maintenance personnel. In order to figure this out, they would need to steal first some of these yellow cards and analyze the data on them, before they can fake a card which will be accepted by the computer.