Fridge Logic: How did Scorpion obtain jets of his own to fight against the Dragon Jets?
The very existence of more raptors in "Acid Tongue", when it was established since Mortal Kombat II that Reptile is the last of his species. Note that Khameleon and her backstory didn't exist until Trilogy, long after this show ended its run.
The Sub-Zero/Smoke episode, two-fold. One flashback shows Sektor and Cyrax as humans, with Sektor as a large black man and Cyrax as a chinese man. Just reverse their races and the cartoon just nearly called it right.
Furthermore, Sub-Zero's Mortal Kombat 3 costume in Mortal Kombat 9 actually looks more like the Lin Kuei uniform he wears in one flashback of the very same episode as well.
One of the missions in Mortal Kombat 9's Challenge Tower is named "It's Kombat Time!" and you play it as Sonya...
Narm Charm: The animation is crappy, the dialog is sometimes stupid and there are lots of really weird things (portal closing device in a police baton?), but there is something charming about this cartoon.
Never Live It Down: Jax having been a fat kid was a thing of one episode, yet it's the thing most people remembers about the series version of the character.
Scorpion. You'd think that by being the poster boy for the entire franchise, a formidable rival to Sub-Zero and described (and shown) as a huge threat by the team would warrant him more appearances, right? Nope, he's gone by the second episode, never to be seen again.
Rain never fights the heroes again, despite clearly intending to do so, not even putting in an appearance for the season finale.
The Smoke subplot vanishes after his introductory episode, and nobody really mentions it again.
Unintentionally Sympathetic: Raiden is clearly meant to come off as an overly-aloof and unhelpful jerk, but the way it's presented instead comes off as everyone on the team being ungrateful dicks to him.