Veterans have probably encountered this already, but whenever a modded skill grants bonus stat points, the game can sometimes crash when you spend stat points. It seems to have something to do with checking equipment pre-reqs.
The bug has been known for a long time, so I guess Runic won't be fixing it.
Anyway, my two bonus classes heavily use bonus stat points. You can avoid the crash by unequipping everything before spending stat points. If you feel lucky, you can just save your game first and hope it doesn't crash.
That seems to be the only problem. Bonus stat points are nice to have, so I'm keeping them.
Hey thanks for this tip MTaur!