Continuity mistake: When Rocky and Colt go to the bathroom to attack Hammer after he drank the laxative, Colt thrusts a plunger to Hammer's face. As Colt thrusts it backwards, Hammer's face gets pulled forward, sending his ponytail over his head. In the next shot his hair is neat and tidy, not over his head.
Continuity mistake: During the part when Rocky, Colt, and Tum Tum are in their room, Tum Tum is playing Nintendo. You can see he is playing Super Mario Brothers 3, he beats a level and then starts singing Rocky loves Emily. When Colt says "mom's coming" Tum Tum turns off the game but its at the main menu when you first start the game. You can't go to the main menu without resetting or turning the Nintendo off and on.
Continuity mistake: When the boys and Emily are riding their bikes to school, the boys and Emily get split up. Emily finds herself running into the bullies and their bikes. The bullies steal her bike. But, if you watch Emily riding her bike before it is stolen, it is a mountain bike, and it is a kind of white/purple colour. When the bullies are taking it away, it is no longer a mountain bike, and it is bright pink.
Continuity mistake: When Fester, Marcus, and Hammer first enter the room with Emily as a hostage, it shows Fester holding her with his left arm and his right is holding the gun against her head. When the shot changes, he's holding her with his right arm, with the left holding the gun.
Revealing mistake: At one point during the big ninja fight scene at the beginning of the movie, the grandfather grabs the arm of a ninja holding a katana and bends it forward. Not only does the katana bend like rubber here, but after he knocks the ninja out and it falls to the ground, it bounces up and bends even more.
Continuity mistake: When their Grandfather is coming home, his 3 grandsons (his ninjas in training) are hiding in the yard - one of them was in a tree above where he parks his car. The 2 ninjas in the yard come out of their hiding places acting like Ninjas (jokingly) and the one in the tree jumps out onto the ground (about a 15 ft drop...this is one big tree...) and since he's a ninja, he apparently can do this safely. The thing is though, he lands with perfectly straight legs.
Continuity mistake: During the scene where the main teenage bad guy and his two friends are holding up a convenience store, he gets a phone call from his uncle, about kidnapping the 3 ninjas. His uncle says, "here's the address." But he never actually gives it to him.
Continuity mistake: In the beginning of the movie when Maury and Snider are speaking, Snider at one point whistles for his car or something. In slow motion you can see he never puts his fingers to his lips, he puts his fingers to his chin, obviously he can't whistle so he did some bad acting and faked it.
Plot hole: Just after Snyder escapes the FBI sting, he is yelling at Brown about the FBI cop being Sam Douglas. If Snyder knew the guy standing outside the car is his former partner's son-in-law, why did he continue with the business transaction as though he had never before seen and/or met Sam Douglas?