In "The Princess Most Fair", all the dimension-hoppers take getting gender-swapped pretty much in stride. This makes sense when you consider that they've also been things like stuffed animals, giant babies, monsters, and sports equipment; Those were far from the oddest forms they've taken on.
"Number One, Number Two" might not just be a Pun-Based Title. It could also be that Larry is Rippen's number-one(best)number-two(minion or possibly friend).
Why does Rippen zap in as the cowardly but non-villainous Cute-ling mayor in "The Ripple Effect"? Because the actual "villain" in that situation was Penn, who already left the dimension, so Phil had to choose the closest alternative. The mayor is literally a Designated Villain.
The decision to have co-creator Sam Levine voice both Phyllis and Phil makes a lot more sense come the reveal in the finale that they're beings (or, a being) from another plane of existence that have been manipulating events for both the heroes and villains.
In "3 Big Problems", before they evacuate the city, Penn accidentally squashes City Hall and the TNT museum. People may well have been hiding in there, especially City Hall, which is usually a busy establishment. So yes, Penn Zero the part-time hero probably accidentally killed people.
The Part-Timers replace existing people. How did the Gingerbread men react when Rippen and Larry zapped back out and one of them was just a head with a shattered body and the second had been almost completely eating himself? Best we don't find out.
In season 2, it's explicitly revealed that the replaced denizens black out, and don't remember the recent events for days afterwards, wherein second-hand accounts and reasoning fill in the blanks. Hope that gave the elves enough time to try and bake the Gingerbread Man a new body, or he's in for one unpleasant surprise when he regains consciousness.
In "Cereal Fugitives", The Milkman once again tries to flood everything in milk, only this time he crashes a train into the dam, which wouldn't be so bad outside of normal supervillain activities, except the train is sentient and no mention of the train is made after the crash.
As shown in "Rootilda", newspapers — and by extension paper — exist in a dimension populated by anthropomorphic plants. Paper is made out of trees. Think about it.
Hey now, just because there's anthropomorphic plants doesn't mean they kill sapient creatures to make paper. It's probably more like how beef and chicken is made.
Sashi's violent tendencies are a tad...unsettling. I mean this is a girl who's disappointed when a mission doesn't require beating people to a pulp or blowing stuff up. She...might not take retirement well.
In a similar vein to the above, the popular AU concept where Penn and Rippen and their teams have reversed alignments is freaking terrifying to contemplate because Penn's team would be just as competent only evil while Rippen would be a complete Failure Hero.