I've run into a few problems:
1. Sudo-san crashes in all browsers except Internet Explorer. It is very annoying to almost complete a game and lose all my progress.
2. As another user has mentioned, music turns on intermittently so I have to "turn on" the music again in order to turn it off.
3. I can't use the enter key on the number pad to enter values into cells, only the return key on the main keyboard
4. Every game seems to have a bunch of cells with "ghost" candidates. That is, I haven't entered any candidates but they are nevertheless there and they are often very incorrect. (Example: shift+S says "1 4 7", X says "5 7 9")