Ass Pull: The Shadow Priests come out of nowhere in the finale and can deflect or counter any attack with a wave of their hand, can outfight everyone, and the only thing that gives them pause briefly is Shang Tsung's soul steal. There is no story context as to why they are so powerful and no reason how they are immune to everything. Shao Kahn just summons them and they walk through the entire cast, killing everyone except Raiden.
Designated Hero/What an Idiot: Pointed out by Phelous in his reviews of the series, some of the actions done by the main trio are either or both of these tropes. For example, Siro trusting two women he just met with the crucial task of blowing up a Kreeya hive....full of babies.
Harsher in Hindsight: The ending to the show, where Shao Kahn kills everyone, is oddly prescient of Mortal Kombat 9, which ends with Shao Kahn killing almost everyone. In both cases, Raiden unwittingly caused the destruction and Kahn used super-powerful proxies to fight in his stead instead of fighting himself.
Informed Wrongness: As Phelous pointed out in the episode Thicker Than Blood, Siro had every right to be cold towards his ex-fiancée since she cruelly left him for his brother. However, everyone acts like Siro is being the Jerk Ass in the situation. Phelous usually makes Siro out to be a JerkassIdiot Hero, so the fact that even he is siding with Siro here says a lot.