Was it Kill the Snitch? That bug has been around awhile - I have a theory it has something to do with the order of opening gates, like you can find all the keys, but always open them in order and I never get the bug.

Been in the game for awhile now, seems most common on kill the snitch. Usually when it happens you can find enemies stuck in or at the elevators and some of the gates that require the keys can be phased through.