The reveal in "The Invasion, Part 1" that Irma was really a Kraang in disguise. Some fans found the twist to be funny while others hated it because it came completely out of nowhere with no foreshadowing except for one part in "A Chinatown Ghost Story". It requires a lot of suspension of disbelief to buy that she was a robot the entire time and a lot of die hard Irma fans are clinging on to the theory that the real Irma was replaced by a robot until Word of God proves otherwise.
The fact that the Kraang as a whole have seem to have replaced longtime Big Bad Shredder as the main villain of the entire series is divisive.
The end of "A Foot Too Big" where after Donnie comes to the realization that he's been too much of a Stalker with a Crush towards April and apologizes, saying he'll lay off and then she kisses him on the lips. Some fans are crying foul about the mixed messages April's giving by her response while others are happy for their ship. However, there are still fans who are just pissed off at the writers/execs for clearly trying to drag out the love triangle.
April manages to do it again just two episodes later in "The Croaking" in which she acts as an instigator towards Mikey's bad behavior. He trashes the house multiple times (making a mess with thrown around food, wasting said food, AND breaking furniture) in which his brothers understandably get mad and Raph leaves him to clean up the mess. When Mikey runs away from the group April blames every other member but herself, trying to claim the event was caused by mistreatment that was never shown onscreen. She then takes it a step further and unrightfully yells at Raph for being "inconsiderate", despite the fact he had to take up a lot of responsibility after "The Invasion" and was acting as a Reasonable Authority Figure when he decided to make Mikey clean up his mess. All of this and the fact that her words seemed to genuinely hurt Raph has caused... negative reactions to say the least.
The show being very Merchandise-Driven and, seeing as that influenced both of the previous TMNT series, that's saying a lot. Every single episode either introduces a new mutant or mutates a previously established character even if they're already a mutant in characters like Bradford's case, and even ones that don't somehow find a way to get a new form or costume in for one of the characters which appear in the toyline a few months later. While not so bad in more story-centric episodes, it also has led to many Monster of the Week filler episodes, most infamously the first third of the third season, which derail the story completely just to bring in yet another mutant. Combine that with the number of times the show has gone on hiatus and it's led many fans to start losing interest.
To a lesser extent, it becomes relatively obvious that they try to dress up the Turtles with their various outfits at least once a season (most notably their LARP outfits and Mikey's Turflytle costume) to promote their Environment-Specific Action Figure, which often leads to filler episodes and Big-Lipped Alligator Moment to justify it.
Seth Green's voice for Leo. Whereas Dominic Catrambone managed to sound almost exactly like Jason Biggs, Seth Green sounds nothing like him via his voice being borderline baritone compared to that of Biggs' own. Some don't mind it while many others do. At the very least, it's given a reason for why it happened in contrast to many other cartoons that change voice actors without the in-universe characters noting the change: The Shredder damaged his vocal cords to the point of being unrepairable.
While "Annihilation: Earth!" was well-received by both critics and fans, there are still some people who feel divisive about the way the episode ended. A portion of viewers feel that the ending was rushed, the Fugitoid's appearance was a blatant Deus ex Machina, and that the show went way too far by destroying the entire world in the span of five minutes and killing off every single recurring character, in a way that some would argue was done for shock value. Others are perfectly fine with the ending and praise the writers for being able to go that far, for adding the Fugitoid to the cast, and for finally moving past the Kraang invasion arc and starting the Triceraton and space arc in season four.
Karai's mutation. Some fans hate it due to the fact that it came up simply to keep her and Splinter apart per the status quo. Others hate it due to it being a large deviation from the comics and other versions since Karai has never been portrayed as a mutant, with some feeling it's a cheap gimmick of adding yet another mutant to the toyline, not helped by the fact that a figure was indeed announced not long after the change happened. Others are fine with it, as long as they feel it can be eventually cured down the line, and a few other like her new form because it's surprisinglycute, and puts her in the same acceptance club that the Turtles and her father Splinter are in.
The various hiatuses, especially in season four. Fans are starting to lose their patience and beginning to wonder if the show's even worth waiting for considering the sheer amount of times they happen. It’s not helping the fact is that sometimes only four or three episodes will air before the show takes a break for well over two months. Other fans, however, don't mind the various breaks; given the quality of the show and how much time and effort it takes for each episode, some fans assume the hiatuses are necessary for the sake of ironing out any errors. Said fans also realize that as the show progresses, more characters are introduced, and more fight scenes occur, thus resulting in more time for animation for said scenes and characters. Then, there are the fans who do have a problem with the hiatuses, but put up with them and just binge-watch each season after they're complete. Some fans don't even notice because they just wait for it all to come out on DVD.
The death of Master Splinter in the fourth season. A lot of fans were heartbroken and devastated over his death—especially since he was Killed Off for Real this time and only returned for season five as a ghost. Meanwhile, critics praised the writers for taking the show in this direction and not being afraid of changing up the status quo. However, some fans felt indifferent about his death, as this was the fourth time the show has "killed off" Splinter, and said fans found it difficult to get upset over his death when they already experienced the same emotions three times before.
The transition to short arcs for the duration of the fifth season. While some fans are pleased that this will prevent Arc Fatigue that has plagued the series since its' beginning, other fans see it as a sign of failure on the writers' part since they've been unable to maintain long story arcs.
