It's not exactly a bug, but I've noticed that when there player count is low (like under 10 players), the automatic team balance massively favors the protecting team. I've even gotten to see 4 police + 3 security + the president + the vicepresident vs 1 terrorist.
You need to take a look at that, because it happens constantly, even when no VIPs (who can force reclass) are online. And I don't think it has much to do with people quitting and messing up the balance, because if that was the cause, it would affect both the protecting and attacking team indistinctly.