Let's list them!
Getting level on a pet you really don't want to.
I agree about the TC one... specially if you go out of your way for an MKB.
The zapper giving you 4-5+ useless zaps in a row (ex: Gender changes and hunger/happiness filled back to back to back)
Echoing what said about levels. Wait 309094 years for an Oracle Quest only to be rewarded with 5 Levels omg! DX
[tot=Ninja]
Getting 3 levels from the oracle, bringing you to the next training bracket
... There's more, but I can't think of them right now. 8D
god pet reorder
i have so much hate for that
I really wish they would make the images smaller on that page! It's such a pain to have to reorder it when it takes like 5 years to scroll to the bottom.
Getting a tc slot random event for pets that don't need tc slots 8(
LACK OF CONSISTENCY IN PET COLORS.
I want an actual turquoise color. D:
I just want a cute banana yellow. :c
I hate that so much... or it's worse if you have a pet TC finished all slots are used up, you're happy with it... then BAM that pet gets another slot you didn't want/need.
We do need a cute little pastel yellow, yes!
Also getting EVERY EXPERIMENT PET BUT THE ONE YOU WANT while zapping. :c

pet groans and gains stat
THAT'S NOT MY BATTLE PET. That's not even my "I might make you a battle pet". >_<
[img align=center]https://i.imgur.com/tGcldDF.gif[/img]
I thought they changed this semi recently so that it will go to your battle pet?
Pet Zapper making hunger / happiness or nothing at all zaps
If you get a new Pet it totally messes up your whole Pet order so Pets you had on 2nd place end up somewhere in the middle etc etc.
MKB only giving 1 Slot
This are the things that annoy me most.