I've been having the exact same problem. It happens when the watch tower itself takes damage, not the entire conning tower. When you pull up your damage control screen and click on the conning tower, even minor damage to the watch tower will trigger the crew to mass suicide on the tower. It'll wipe out everyone except those manning the helm. If you get a repair team to fix the problem, it'll kill officers instantly and all crew members in the slots beyond the first one to the far left. Sometimes the conning tower won't show any damage on the diagram but if you click on it, there will be a list of damage showing in the report. It happens most often for me with the Type IXD42 and the IX/3 conning tower in career mode from 1943 and on. Probably the easiest way to trigger it is to get strafed by machine gun fire from a PT boat or a plane.
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