If you respec from BM to MM (or I believe to SV), you may end up with a pet talent tree like this:
The pet talents used with the BM spec remain in the tree, preventing the use of the new unspent talents on, say, Thunderstomp. The BM talents only exist in the talent tree and not in the pet’s Spellbook, though. Essentially, you are left with an animal friend that does not have and cannot obtain any of the pet talents you assigned to it when you were BM.
There is an easy fix: just go to a pet trainer and reset your pet’s talents. This is also the official fix.