... No I didn't take them.
BUT, could gen another character to do so. Give me a couple days. :/
Do you know Abandoned Ship is repeatable quest? You don't need to use another character to complete it again.
It's the last compartment on the portside if the ship; Inside is the safe with the case containing the documents.
The problem is the door to the compartment itself; It will NOT unlock. The critters inside cause it to be unpickable. I can't pick the lock, so I can't kill the critters. (This really is an old problem, going back to the 2238 days.)
You should provide screenshot ASAP because I don't get the problem you are talking about. I can enter the "safe" room without any troubles. Don't you forget about taking keys?