I tested this issue on three different PCs: using Alt+Enter to toggle fullscreen and it didn't crash on any of the computers. When you use Alt+Enter to toggle fullscreen the program does read it as a button press so it will try to interact with whatever you were doing at the time.
To solve this issue I would back up your save files and redownload the zip file. After reinstalling the game: copy in your saves and you should be able to continue enjoying the game. If the issue still isn't resolved you can e-mail me a copy of your save and I can see if it's an issue with the save file itself. My e-mail is email@example.com.