Stupidity: When the Turtles are leaving the junkyard they rescued Raphael from, the incredibly agile ninjas of the enemy clan can't simply jump over a van, or just slide over the hood. (00:54:00)
Sammo
Suggested correction: Remember at the beginning of the film, one of the clan members is angry that so many of their members were arrested. They have been looking hard for new recruits. The new recruits won't be as good right away.
LorgSkyegonI am sure even my mom could slide across the hood of a parked car if need be.
Sammo
Plot hole: It's never really addressed or explained how Shredder survived his death in the previous movie from being crushed in a garbage truck.
Rob245Suggested correction: It didn't really need to be addressed, and thus is not a mistake. His hand emerging from the junkyard is enough to show that he survived his apparent demise at the end of the last film.
TedStixonStupidity: Leonardo could use his swords to cut the net when Leonardo, Donatello, and Michelangelo are trapped in a net.
Athletic JasonSuggested correction: While trapped in the net, it would have been quite difficult for him to draw his swords from the sheath on his back.
LorgSkyegonWhile that is true, him not attempting to reach his swords makes him look like a fool that forgot he has swords.