* BizarroEpisode: Many of the guest issues in volume one ended up like this, with varying results. Especially any issue by Rich Hedden & Tom [=McWeeney=].
* DorkAge: The "guest-writer" era that came from #22 all the way through #44. Although there were some well-received stories, for the most part the majority of them are considered a huge step down in quality, often portraying the book as LighterAndSofter and overly comedic (as noted by Bizarro Episode up above) rather than the dark action-adventure tone. Eventually [[WordOfGod Eastman and Laird]] themselves stated that only two issues from that era (#27-28) [[CanonDiscontinuity were canon]].
* EnsembleDarkhorse: The Shredder, who was only just a one-shot StarterVillain [[spoiler: that died in the first issue]]. Several issues later, he was brought BackFromTheDead and most incarnations of the franchise have since depicted him as the BigBad.
* SeinfeldIsUnfunny: The amount of violence, especially in the early issues, were pretty shocking for the time, but considering how tame they are compared to several mainstream comics nowadays, newer readers may not be able to see why they made such a big deal.
* WhatDoYouMeanItsNotForKids: No thanks to the 80s cartoon, which is far more well known, this comic could be mistaken for another child-friendly comic when it's bloated with violence and gore.