(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 fatherAutumn 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 supervillainsWhat else could those junior Mad Scientists become? They know how to make Dynamite at the age of ten.
- I can identify some budding Neids and Hoffnungs already.
Deirdre Linkletter is actually a perky robot.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).
Tiffany is a Time LordThough 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
Autumn will learn that Information Brokers are usually Library Science majorsAnd be a bit more enthusiastic about her genetic predispositions.
- Also that is true in real life.
The On-Cue Ball's apparent sentienceAfter 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.