Havn't notice Prowl just dissapearing, what i did notice was that immolate ticks would eat the prowl buff tho, i havnt played around with the cinder kitten enough to notice any other shenanigans. Maybe this is whats happening to you aswell, took me a while to realize why the prowl buff would seeming...

I have the same issue, and whats doing it for me is the alliance guild page/herald (im horde). Learned those pets on an alliance alt, but they dont show up as learned on my horde character, but they still count for the achievement, same thing with horde guild page/herald on alliance characters