Yeah, I do have sabotage + malfunctions enabled, but the first time it happened I was actually on a Naval Academy mission! So I don't think it should have been any malfunction. But, if malfunctions can happen in Naval Academy missions, I don't understand why there is 50% chance that theres a fault with the attack periscope and not something else!
EDIT: I have tried restarting the game, but I still got 50% chance of a ATK periscope failiure!