The common rules are:
1. Don't save within 25km(maybe more) of ships.
2. Don't save submerged.
3. Don't enable any mods while on patrol. Only enable mods while in port.
4. Don't save near land.
I think there are a few others as well.
Unfortuneately, you have to try a previous save and hope that works, maybe even start the patrol over.
Myself, I've been very lucky until yesterday. I break all the rules with abandon and have only had one possible save game crash until yesterday.
I believe it was caused by #3 above, but I'm not sure.