During the plane crash, several shots are reused from earlier episodes including one of a suitcase falling past Face. In the shot, Face was dressed as a priest, and you can see his suit jacket. Face wasn't wearing a suit jacket a minute earlier, and it is highly unlikely given the circumstances he would chose that moment to have put one on.
Although the plane is a Beechcraft King Air, as Murdock is starting the plane the view facing Murdock (the 2 "Propeller Unfeathering" buttons are seen above the instrument panel) and the interior view shows the instrument panel of a much older Beechcraft C-18S.
When B.A. wakes up on the plane shortly before they crash, Face leaves the cockpit to buckle up, leaving the curtain behind Murdock and Hannibal half open. After an exterior shot, the curtain is neatly fully closed. It's unlikely, especially under the circumstances, that anyone would come back to close it.
At the beginning when Hannibal breaks through the window, one can see it is a stunt double.
The bullet holes on the plane door are not actual holes, but are stickers or painted dots.
The plane's registration starts with an "N", which is a US registration. It is unlikely this plane would be used for long haul flights like a transatlantic route.
In the final fight scene Face shoots at one of the bad guys with a sub-machine gun. When the bad guy runs to avoid bullets, the next shot, where he's leaping over stairs, is sped up.