The Turtles' frequent use of Totally Radical dialogue is often mocked. However, in the first episode, Donatello tells April that they learnt all about humans by watching a lot of TV — where they probably picked up the dialogue.
The Turtles' interesting tastes in pizza actually make a lot of sense when you realize they probably don't have human taste buds or tongues.
And they've never been around human beings until they met April, so they probably don't know what food combinations are considered socially acceptable.
The organization H.A.V.O.C. from season eight becomes somewhat disturbing when it is revealed that they capture people and turn them into mutants. Some of the H.A.V.O.C. members may have also been humans that were captured and mutated, then forced to serve Titanus against their will.
Also from Season Eight: Krang basically committed planetary genocide (for incredibly petty reasons) if what Bezerko said is true. Talk about a Not-So-Harmless Villain!
"Donatello's Duplicate" becomes a bit more unsettling if you consider that Donatello's clone had free will. Donatello just destroyed a living, sentient being.
A Fridge Tear Jerker; it's been pointed out at least once by a fan (fanfic here) that the clone had Donnie's intelligence, memories and skills so why wouldn't they had similar opinions? This could mean that the other turtles might genuinely believe that any insults the clone hurled at them are genuinely what Donnie thinks of them.
More Fridge Horror from the Red Sky seasons occur in the ninth and tenth seasons, which reveals that the Turtles' mutagen has become unstable, causing them to periodically become monstrous behemoths. If longtime viewers remember the episode "Michelangelo Meets Mondo Gecko", where Mondo Gecko was a gecko exposed to the same mutagen that mutated the Turtles, this means that somewhere Mondo Gecko is also becoming a monstrous beast every now and then. It doesn't help that the Turtles don't seem to remember Mondo Gecko and we only see them cure themselves and try to cure their new ally Carter.
Don't forget Bebop and Rocksteady. They may have been eaten by the creature that destroyed the Technodrome in "Turtle Trek" since we never see them again after that episode.
The uptight, gullible original elders of The Foot Clan were either killed off by the student they placed in charge when they kicked Yoshi out, or were forced to watch as their clan's members were replaced by soulless machines and all their works were made the front/vanguard for an alien invasion.
Media Watchdogs forced the animators of the first cartoon to change Michaelangelo's weapon of choice to a grappling hook late in the series, claiming that nunchuku were too violent. It didn't seem to bother them that two of the Turtles used blades.
Could be that nunchuku are somewhat easier to improvise than swords and blades. All you need are two weighted ends and a small length of string, and it could actually hurt. Toy replicas are available in stores, but these are specially made with heavy foam padding or hollow, vacuum-formed plastic.
On the other hand Bo Staff's are the easiest to improvise out of all the Turtles weapons.
Krang was apparently banished from Dimension X, yet goes there quite a lot.
Shredder sure does know a lot about USA Culture (and even acts like he's American) for somebody who supposedly lived most of his life in Japan.
Shredder is smart. He adapts quickly.
In "Cowabunga, Shredhead!" how come Michaelangelo!Shredder never finds it odd that there's apparently another Mikey around?