Kaluen Olly,
This bug is often discussed, actually I think someone mentioned a way to alleviate this issue, Im not sure tho', you
can try the search engine thingie and maybe find those past posts. Personally I have playing SH3 since its release for hundreds of man hours and almost always save submerged ( I laugh in the face of the "bug" gods) and have never had this issue occur. Usually I get the crew with gills syndrome ..where your watch crew is manning the bridge at depth.
If you cant reslove this issue just save often...and under different names not the same over and over. GL and hang in there!