These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
A Leitmotif, first heard in "The Fire Temple", which appears to be a theme for Lord and Lloyd Garmadon as it plays in scenes where they are together. Quite fittingly, it's a tragic-sounding melody due to the destined battle between father and son. It also receives an espeically epic arrangement heard in "Fall of the Green Ninja" when Lloyd pleads to his father to help him fight back against the Overlord.
The Serpentine, especially Skales and Pythor, receive extensive treatment of this by the fandom. Somehow, these bloodthirsty and treacherous villains are interpreted as innocent Woobies who only want a hug.
Season 3 seems to be supporting this (Pythor excluded).
Lord Garmadon suffers from this to a degree as well, though it's more justified given how he is depicted as a Tragic Villain from Season 2 onward.
Ear Worm: The opening song — "Nin-jah-go, Nin-jah-go!"...
Ho Yay: Although it doesn't happen often thanks to the show's Target Audience, it still occurs on occasion.
In "Can of Worms", Zane rode on Cole's back the entire way up a mountain, despite the fact that he was more than capable of doing it on his own. Then, there was this particularly lovely exchange upon facing one of the Serpentine Generals.
Skalidor (to Zane): Look who's calling who pathetic... Pinky.
Cole: Only I call him Pinky!
Not to mention in "Darkness Shall Rise", there was this:
Narm/Narm Charm: It's a little hard to take the plot twists seriously when the characters are still cute-as-a-button minifigures. This doesn't take away awesome moments however and the characters usually act normal and not like they live in some toy chest.
The scene where Skales tries to capture Lloyd...by slowly descending down on a window-washing lift... outside. His knock on the window during the same scene only adds to the Narm factor.
Grand Sensei Darreth for being The Load. He was always creating problems that the ninjas had to solve, such as getting kidnapped by pirates in a Too Dumb to Live move, and failing to pay his rent so the ninjas have to enter a racing competition just to pay it off for him.
Ugly Cute: Some of the Serpentine fall under this on certain occasions, when they're serving as a comic relief rather than serious villains.
When Lord Garmadon is possessed by the Overlord, something about his face looks... off. Given that this series gave us cool reptilian faces such as the Great Devourer and, eventually, the Overlord's final form, there's something not quite right about the design of this face.
Villain Decay: Lord Garmadon, starting in the second season. In the first season, his personal greed caused him to betray his father and turn him against his brother Wu, and even in death, he became an evil mastermind who overthrew the lord of the underworld and spent years plotting and playing everyone involved to escape the underworld and have his revenge. In the second season, he is recast as a Tragic Villain who did not choose to be evil but was forcibly turned evil by the venom of the Great Devourer. When he isn't lamenting how Being Evil Sucks, he acts as a goofy Card-Carrying Villain who brushes his teeth with knives, laughs at sad movies, and literally eats evil, a far cry from the Knight of Cerebus he was in the first season. It's odd to see Lord Garmadon change from the dark and sinister plotter from the shadows in season one to crying and whining and accusing the ninjas of cheating in a racing competition. In the third season, Lord Garmadon is even usurped as the Big Bad by the Overlord, the real evil mastermind plotting and playing everyone involved.
Zane's No Social Skills, background as orphan unlike all the rest, and frustration others have because of his different ways can make him this at times.
If the new season continues the way it is, they might as well change the season name from Ninjago: Rebooted to Ninjago: How To Torture Zane.
Lloyd is also becoming a woobie. First he was tricked and kidnapped by Pythor. Then he is thrown into his prophecy of defeating his father and devoting most of his life to training. Finally he has quite literally has had his entire childhood taken away from him.
In episode thirty, shortly after Pythor captures him, Lloyd is forced to watch as his father is shoved into the ocean. Yikes.
Iron Woobie: Lord Garmadon is sort of becoming this as season 2 goes on.