Precocious (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.
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 MadScientists become? They know how to make Dynamite at the age of ten.
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 (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.