It's user's, seriously, nothing worse than having to deal with an Apple customer, PC user's are > Apple user's.
If you mean actual software problems, then software compatibility is the big one, both with applications and games. Sorry using different software that is "similar" doesn't count as being compatible
Also the way hitting the red X doesn't always close applications, and some make you go into File->Quit.
The minimize to dock feature, doesn't give a window name that you can instantly recognize ala windows, it just gives you a thumbnail.
Lack of right click, I know you can get a two button mouse and then it will give you a right click context menu, but as standard your just given the crappy single button one.
Adding extensions to the web browser, had to install flash the other week, wouldn't install, looked like it installed, but didnt, had to tell the browser to be opened in "sapphiron" mode or something like that (in get info, for Intel compatibility or something)