I said that about a month ago and no one believed me. It still happens when im fighting for example Kura Thunderhoof in Garrison, with my standard team of 2 25s and a leveling pet. At the end of the fight sometimes I get full 4Kish pet xp and other times only around 2.7K xp.
I had a post here in the forums Pet Battle Dailies reward only half pet xp? - #5 by Kolniður-stormscale