Canon Discontinuity: Fans of the movie who dislike this series (which are most of them) tend to ignore it. They have arguably the help of the canon itself, as the series's nature as a sequel to the movie has never been stated outright and can be easily ruled out.
Cliché Storm: Quite spiritedly averted in terms of characters, as the episodic ninjas have a very high HSQ based in appearance alone, but the plot itself is rather formulaic.
Ear Worm: Some of the electro music used in the fight scenes.
Narm: Both the Hiruko and Kimon clans hit it hard. Most of their shinobi are so decidedly bizarre and crazy that it's sometimes difficult to take them seriously.
Sequelitis: Although the series has its fans, it is widely considered as not up to the standards of the original movie, in a big part due to Tough Act to Follow and in another part due to the deep changes in tone, setting and characters's personality. Most of the fans prefer to consider it a separate continuity.
Special mention goes to the fact that we rarely see two or three ninjas from the same side together on screen, so we are deprived of the interesting interactions they could have with each other.
What an Idiot!: Dakatsu. Not only he offers Rengoku his sting tail in future exchange for the stone (what in the heaven would impede Rengoku from killing him with his own sting instead of carry out her part?), he also idiotically demands her to perform a surgical procedure on him (what would impede her to kill him in midst of the surgery?) without knowing all of Rengoku's skills. The result is, predictably, Dakatsu being unceremoniously killed.