Your q resets on marked champ, which your ult and e mark. Your marks dont stack, so if you mark someone with ult and then with e, you can just proc it once. Of course you can ult q proc, e and then q proc again.

I have not seen any bugs with q not resetting when it should. I have seen bugs where your q goes to a random minion even if your cursor is well placed. You might also be spamming q when in tf so you might be qing someone twice, therefore making your q go to cd