Arc Fatigue: Minoru vs. Tabuse of the Genesis tournament lasted way too long for its own good. Hardly anyone found the "pro-wrestling" gimmick easy to take seriously.
Big-Lipped Alligator Moment: Saizo and Jiraiya's fight is seen as this by nearly everyone since it features two ninjas (though one turned into a BJJ fighter later on) fighting in a stance completely different from everyone else, named attacks, ninpo (dirty ninja tricks), and fire breathing!
Crazy Awesome: Kasumi, being a bona fide ninja with all the related powers (somewhat) in a series with realistic fighting, can be either this or Bunny-Ears Lawyer.
Pedro. The guy's an unrepentant rapist (or at least one who's never paid seriously for his crimes), has attempted to sexually assault Minoru three times, deludes himself into thinking that Minoru's being a Tsundere towards him, and later has the gall to consider Nana, a girl who has been Minoru's best friend for years and stuck with him through thick and thin, a "depraved stalker woman".
Strangled by the Red String: Some of the early couples can look like this given how little development they were given initially. Mutou/Haruka and Mamiya/Yukiko were the ones that stood out the most. While the former advanced pretty quickly, the latter is actually the slowest-growing couple.