Script stopped loading while managing PC...

So the script froze while I was managing my PC and I had picked up my LVL 60 Lucario...it saved the game and when I came back, the Lucario had disappeared - probably as it was not in the box or in my party.

Luckily I had backed up my save and was able to transfer my Lucario over from another save but had I not backed up, that Lucario would be gone forever. Is there anyway to prevent "auto-crash-save"?