Happened to me last night for the first time w/ patch 1.4 and TM 1.7.6.
After firing a spread of 4 torpedoes at a large freighter, with two missing and two duds, I went to battle stations and surfaced. Selecting my target w/ binoculars I designated it as a target for my deck gun, then gave them "fire at will", and waited... and waited... I looked over the top of the bridge and there was no one manning the gun. When I went to the crew management screen, not only had the deck gun crew vanished but so had the empty boxes I could assign people too.
Quit the game and had to go back to an old save to get my gunners back
