Same thing has been happening to me since I started playing SH4 again a few days ago. Fresh install on a new computer, no mods, not even JSGME, 1.5. Happened twice on my first patrol on a fresh 1941 campaign and again when I started a new campaign (it borked my save) on my third patrol. Knew better than to overwrite my save file this time, but really now, I had no idea this occurrence was so common in stock.
I still want to continue my stock campaign because I never really played vanilla before (and now I remember why) so we'll see if it keeps happening. Three times in four patrols seems crazy to me. I suppose I could play stock+RSRDC but the thing with that mod is that once you know all the task force movements from delving into the files to observe a bit of history the campaign becomes boring because you feel like you're playing a scripted game. Do I sit here and wait for the two unguarded cruisers that I know are gonna come through here and score some free tonnage or do I purposefully ignore that part of the ocean for a while? Hmm...
Well, I guess the solution here is the same for all buggy messes: save often!