Revealing mistake: There is an obvious stunt double for Grandpa during the fight scenes.
Other mistake: When the three ninjas are kidnapped and locked in that room, Tum-Tum is complaining about being hungry. Later on, before the fighting match between Grandpa and Snider, Tum-Tum gives Grandpa jelly beans. Why didn't Tum-Tum just eat those before?
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 Colt and Rocky take on the two bullies in a basketball game, Rocky takes a backwards shot from the right side of the basket (obviously shooting towards the left). Then the basketball goes into the basket from the left side.
Continuity mistake: When the big Asian guy throws Tum Tum off his neck, Tum Tum is already horizontal. In the next shot, he turns it into a shoulder roll. Impossible.
Continuity mistake: When Emily goes to meet Rocky at his house to ride to school with him, she goes into the house through the door in the garage. When Emily, Rocky, Colt and Tum-tum walk out that same door, the garage is only just opening. If the garage was closed, how did she get in?
Deliberate mistake: During the sting attempt towards the beginning, Douglas confronts Snyder on the roof of the building. A helicopter rises up from nowhere without making any sound prior to that.
Continuity mistake: When Snyder and Grandpa fight at the end, and Grandpa's sword is knocked out of his hand, it disappears from the mat and isn't seen again.
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.
Other mistake: When Snyder's assistant gives the address to his nephew, Hammer, he tells them it's 623 North Pacheco. When the Boys and Emily leave for school the number on the house is shown as 580, and there is no 623 because they live in a cul-de-sac.
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?
Other mistake: When Agent Douglas finds Snyder on the roof about to escape on the helicopter, Snyder climbs in a rope ladder. Then Douglas fires 9 shots at Snyder. It looks like Agent Douglas is shooting a revolver, which holds only 6 rounds even when loaded.