I'm using a few mods, and yes, the weather is bad on the Bismarck mission. Could be related to one of the wave mods, I can't remember exactly which one I've got running at the moment, I'll have to check it, but that could be a factor.
Also, the hatch got glued shut after the "Mission success" screen popped up and I chose "Return to game" instead of quitting. So there is also the possibility that the game got confused about my sub state after that.
No real harm done though, it was just a single mission. I am wondering if that happened during a campaign if saving and reloading would fix it, or if you'd be stuck on the surface.