Were you leveling it?
I noticed that if you gain a level and your HP goes up, you don't gain that HP after battle.
Example: Your lvl 1 pet jumps to lvl 8 in one battle. You started with maximum 150 HP. At the end of the battle, you level and now you have 550 HP maximum. It USED to be that you'd just have 550 HP/550 HP - but now you will have 150 HP /550 HP. You didn't "lose" any HP, you just didn't automatically get them after the battle like you used to.