Presumably this is a bug, but I sometimes get locked in trap rooms - ones with a chest that spawns a mess of enemies. After wiping everything out, the chest is still shielded and I the door locked. I suspect it might be a geometry issue with an enemy ending up on the outside of the room, given that I've ran into similar glitches while flying out and about, but it's just a theory.

Any advice, other than wait for a patch?

Apologies for the delay answering - we think we've fixed this and the update should be on GOG very shortly!