If you have more than one of the same kind of ability totem in a stack and if you use one bottle,
the whole stack is consumed.

Eg. I have 2 speed totems and only have speed 1 activated already.
If I add it, I loose both speed totems and I only have speed 2 activated. 1 was lost.

Yes, that's not supposed to happen. The totems are not supposed to be stackable.