(Note: Some of these have been suggested in-universe.)
The Pingos really are clonesIt is awfully suspicious that two narcissistic red foxes
of the opposite sex that look similar and are both majoring in Library Science would attend the same University, get married, and have a daughter who's practically the same as them.
- Or they could just be related (hopefully distantly).
Mr. Et is Bud's biological father
Autumn seriously suspected this until she was told that Gene Et and Joseph Oven were cousins (then she got mad because vital information had been withheld from her).
Poppinstock Academy is secretly training the kids to be supervillains
What else could those junior Mad Scientists
become? They know how to make Dynamite
at the age of ten.
How else could she get so much done? Of course that would require Jacob to be some kind of Synthetic
(which would explain how he can stand all the punishment he gets
from his classmates).
Though not a "normal" one, as shown in this strip
she stopped aging after killing her future self and messing around with said future self's time machine. The only explanation is that she was exposed to an extremely high dose of temporal radiation that mutated her into a Time Lady.
The kids' mental disorders
And be a bit more enthusiastic about her genetic predispositions.
It's all because of some very slightly Bizarre Furry Biology
The On-Cue Ball's apparent sentience
After a while, Kaytlyn memorized it's entire list of phrases. Every time it says something that makes it seem aware, Kaytlyn actually deliberately cycled it to that phrase for a cheap laugh
Bud is the control subject for the Doctors Xane's Grand Experiment.
They're old colleagues of Josephs. The families are secretly working together on testing the effects of the two extremes in parental involvement.