The plane that crashes is a Boeing 747, which has four engines, but the reporter overheard in the background describes the aircraft as a twin-engined wide-body.
When Bowman comes out of the lavatory prior to the transformation, there appears to be scratches on the inside of the door already.
According to Marshall Bowman's passport, seen onscreen at about 0:09:12, it was issued on July 23, 1998 and expired on the same date.
When Broyles brings Agent Dunham to see John Scott, Nina unlocks the door with a fingerprint scanner using her right arm. But her right arm is a bionic prosthetic and thus should not have any real fingerprints.