I have had the same problem with my Beast mastery/nature affinity MM in Echo RWZ raids.
Pets that are killed during the pylon take down sometimes disappear and can't be recalled.
Tonight I made it to the bowl without both my lions and one of my howler wolves. I could summon the Dire wolf and the other two wolves all I wanted, but the lions and that one wolf could not be resummoned.
Its happened before too, but usually I only loose one wolf which isn't too bad, tonight was the worst.
It has never happened to me when I didn't summon the pets until we were on the mother ship. I used to do this because I don't have group fly and didn't want my pets drawing aggro from pylon to pylon. I discovered, after a while, that that wasn't the problem I thought it would be.