Her defending Michelangelo's actions in "The Croaking". Did she really think they weren't that big of a deal? Or was she trying to make amends due to the previous episode? On that note, when she says the others don't appreciate Mikey enough, is she talking about just this episode or the whole series prior (which actually does make sense)?
Is Mikey really as stupid and irrational as he seems? Or is he insecure about being compared to his brothers and being "just" the funny guy and said stupid and irrational actions are just his misguided way of trying to prove himself? explanation The show itself has implied the latter on a few occasions.
Is Raphael's skill with animals just a result of not being good with people? Or is he inherently more animalistic than his brothers and father? Whether Raph is "more animal" than the rest of his family is further muddied by his romance with Mona Lisa. His brothers all seem to find it deeply weird that he's clearly attracted to a large alien newt creature, and the other three seem to be solely attracted to human (or at least human-appearing) women.
Another one would have to be on whether or not he's a Stepford Smiler in the third season due to the events of "The Invasion". Was he able to cope with the situation during the third season’s Time Skip? Or is he just putting on a brave face because he's the Team Dadnow and doesn't want the others to worry to much?
There is another interpretation that the fans have for Raph (although this one is at least partially due to shipping). Is Raph's negative attitude towards Donnie's crush (on April) due to his Brutally Honest nature and being realistic over the situation (and not wanting Donnie to get hurt)? Or does he also have a crush on April as well but doesn't act on it because both his brother and best friend are already pursuing her and the comments he makes are meant to dissuade himself as well? Is it just one of these? Or is it all of them? Interestingly, Raphael was originally planned to have the crush before they switched it to Donatello.
Are Casey and Donnie Vitriolic Best Buds? Or is all their antagonism towards each other truly out of spite? note "Race With the Demon" actually implies the former.
Did the Shredder take Miwa/Karai to spite Hamato Yoshi? Or did he do it out of atonement for accidentally killing Tang Shen? On that note, is he doing evil because he knows he crossed the Moral Event Horizon for killing Shen?
Considering his Lack of Empathy for everyone else, does his revenge actually extend to the rest of the world for what happened to the original Foot Clan with Splinter and the Hamato Clan being his main targets? Did he mean to let the Earth be destroyed so it's not just Splinter he ends up killing?
Was Kraang Subprime brainwashed by Kraang like the other Utroms? Or did he willingly join the Kraang? The fact that he can speak fluent English, has some level of independent thought, and was called a traitor by Bishop points to the latter.
When Karai officially starts to go on the offensive against the Hamato Clan, she singles out April as an easy hostage twice, the first time going after her personally and later uses her to test out the lethality of Chrome Dome. Even after Karai's Heel–Face Turn, she seems to hold a level of contempt towards the red-head. An argument can be made that her first kidnapping attempt was out of the false assumption that April is just a random civilian they made friends with, unaware of her importance or that she is capable of fighting back. Does her later animosity come from losing to a newbie like her? After learning the Awful Truth of her origins, does she think Splinter replaced her with April? Or could it be that she thinks some green-horned, American white-girl shouldn't be allowed her family's ancient art?
With his bouts of jerkassery whenever his brothers do something he doesn't like, habit of ordering people outside his jurisdiction around (and yet getting mad at his 87 counterpart for doing the same) and tendency to not listen to others' complaints about the way he does things, it's not hard to view Leo as a Control Freak who wants everything to be his way and hates how the people around him won't obey his orders without question.
