So I was playing through T&R because I lost my game save for the level after this due to the update so I figured I might as well play through it quickly and end it. Well as I save Keyes in the jail cell it went to the ending of T&R where we fly out of the ship.
I had this once too. Somehow I managed to actvate that terminal that ends the level before I went to get captain Keyes. Can’t remember how I did it, and I can’t reproduce it either, but it made for an easy exit.