Just fought a mob in the Underbelly and totems kept popping up in the rotation even though they were in use.

More details would be useful, like the talents you were using when it happened, the number of targets in the area, if you had AoE on, etc.

My apologies. AoE on, one hostile target (PvP was off, it was a rare, the Crazed Mage). Talents 3 3 1 2 2 1 1. Only legendary Eye of the Twisting Nether.

The only oddity of that fight of which I'm aware is that I positioned myself on the platform above and behind the Mage to avoid all its fire. This is also where I was dropping the totems.

I've got it setup now to where it will only ask you to cast Totem Mastery if you are missing the totem buff and haven't already casted it in the last 5 seconds. It's possible you dropped the totems in a bad spot and the game just didn't give you the buff right away / at all.