From what I've read, it's completely random. I've learned to keep a multiple-save rotation going from getting burned on corrupted saves in the past.
Hopefully you can just revert back to a prior save if it happens. If not, then

, and FM10 only from then on.
EDIT: Alright, now I'm curious. Time to do some testing.
Bad news. I simmed four times, changed teams each time after the season, and each time got the debt glitch. The fifth time, I stayed with my team and the budget carried over fine. That really sucks because now you basically have to stay with the same team throughout your career. I guess my only question is: how the **** do you not test that? Seriously.
Well, this game's replay value just flew out the window for me. I love the game on the pitch, but I am really a MM fan, and this just sucks. Oh well, maybe I'll join up with that 4-star max league I saw someone starting up. I get my manager fix from FM anyways...