Haven't played the quick missions very often (love the campaign career too much) but on creating my own found they're very touchy, and mods often give them indigestion. My guess is someone created a mission with a GATO class, install a mod that fixes the missing gauges and corrects some flaws with the GATO, and the mission has a spaz attack because it was expecting something different from what you have now. That's just a wild guess based on the fact that the quick missions didn't crash as often - cripes, was it 12 years ago? - when I first got the game. What might work is editing a quick mission, deleting then replacing the player sub and saving, got a backup file it's worth a try.
"That's an excellent idea, sniper"
Learned that the hard way with one of them dungeons and dragons role playing games back in the 80s - six save files are enough, just keep overwriting them in order. Hmmm, a shiny new piece of armor enchanted to reflect fire spells, try it on, works great! A week and several overwrites later my character is dead, the armor was cursed and can't be taken off without something to break the curse, I have no save games without that armor.
I learned from that if a game has a limited number of savegame slots, make occasional backups of the entire savegame folder just in case.
SH4 doesn't have that problem, it crashes from a savegame file that gets too big, but so far I haven't seen it crash from too many savegame files. Save just before and just after each attack, using numbers to make each save file different is the simplest way to keep track for me. Don't know if it's necessary to occasionally delete some of the older ones, I just do it to keep the list short. The "autosave on leaving (entering) base" files can also be handy, if you're in the habit of editing campaign missions the saves on patrol will crash because you changed something in a mission that was already loaded in the save, leaving the base after reloading an autosave loads all the missions along with the traffic or ships I edited from scratch.
After saving and exiting check the message that tells you how many ships and tons you've sunk so far in this patrol, I generally try to keep it under 400,000 tons per patrol so the megabytes don't bite.