Same thing happened to me. 4 pets de-leveled and 1 reverted back from rare to uncommon quality.
Apparently some data wasn't saved and this meant the pets gaining levels and upgrading wasn't recorded. Sadly it also means we won't get anything from it, not a refund from used stones either, because there is no evidence of these pets ever leveling/upgrading.
It doesn't take long to level pets and if it was anything like with me it would've only been a few hours worth of 'damage'. Hope this hasn't* disheartened too many pet collectors
Edit: *has to hasn't, good lord :p