Are you using a IXD2? There's a bug that makes it crash into the dock walls eventually tearing apart your hull. Otherwise haven't heard of anytimes where the sub will spontaneously combust per se.
If you've added mods during a patrol that can cause all sorts of problems.
If you enable a mod via the JGSME during a patrol it can cause problems as well, will usually crash the game once it loads.
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