Same issue here after upgrading. Managed to fix it without getting too drastic and deleting all my preferences etc. Here's what worked for me:
- Close any open tabs/windows in ST2
- Delete ~/Application Support/Sublime Text 2/Packages/CoffeeScript
- Delete any folders in ~/Application Support/Sublime Text 2/Backup/ which contain the CoffeeScript plugin
- Remove CoffeeScript via Package Manager
- Quit and re-open ST2 (hopefully by now the errors have stopped)
- Re-install CoffeeScript via Package Manager
- Quit and re-open ST2
I suspect not all of these steps are strictly necessary, but shouldn't hurt. I also found that simply moving folders (including into the Trash) didn't seem to help, and that I had to actually empty the trash to get it to "stick", but I also have a suspicion that it might have been because I didn't figure out step 1 until later in the game.
Anyway, I'm happily Coffee-ing again, hope this helps someone.