tl;dr if you try to save with a lot of move commands queued up it will corrupt your save file and crash the game.

So I was in a kill the transgenants in the city mission. My loadouts and armors and mook levels are pretty good so I am not worried about getting caught out of position and losing soldiers. The last transgenant was hiding in a dumpster or something so I did a lot of move commands to search the city and thought to myself "I don't want to have to redo that so I will just save here in case it crashes" which then led to a crash and even more a save file corruption! I tested this out again intentionally with a new save file latter and it was replicable.

I am not complaining because I stagger saves anyway and have a separate file specifically for start of mission vs. mid mission so I lost very little (you never know when your whole strategy will be fubar from the very beginning). An old Xcom habit to be sure. Didn't think it would save me from losing my whole save file though! Should always stagger numerous saves in these old games for just such an occasion as this as you never know when the game will get uppity.

An addendum, after making the test save file to confirm the crash was replicable it looks like that time the game couldn't even scan through save files without crashing. What I did to fix that was go to the gog folder where ufo aftermath is and navigated to the save files. Should be something like:

C:\GOG Galaxy\Games\UFO Aftermath\Profiles\game_q\Saves

I found that test save file and deleted it. I noticed that each save has 2 files associated with it and in the case of the test crash save file only the .vfs was actually present. No .desc. Deleted the .vfs and no more problem for me.

Just leaving this here for anyone who runs into this problem in the future will know what to do.