Other mistake: In the music within the ending credits, the lyrics incorrectly state that Raph is the leader of the group when all Turtle fans past and present know it is Leo.
Revealing mistake: When three of the turtles are playing Trivial Pursuit and Leonardo runs in to announce Splinter is alive, you can see a wire coming out of Raphael's shell. I guess it's for the animatronic head, but it's visible. (00:59:30)
Audio problem: At the climax of the film when the Turtles are about to face Shredder for the first time, Raphael says, "I got him" and then runs to fight. When Raphael falls to the ground, his pair of Sai hit the ground but make no noise. There should be a metallic sound against the rooftop. (01:19:00)
Revealing mistake: As Michelangelo is waiting for the pizza guy, Donatelo cames through the sewer on a skateboard. A view of his feet is shown and his hands swipe across the screen. One of the times they come through his hand is not that of a turtle, but a human hand. (00:09:20)
Revealing mistake: In the scene where the turtles are leaving April's home and stop at the door to say hello before leaving, you can see Leonardo's sword handle bend like rubber, which it in fact is. (00:27:10)
Visible crew/equipment: In the shot in April's apartment where Leonardo and Raphael are arguing about how they should look for Splinter and the Foot, a crew member with an orange hat can be seen ducking behind the table on the left. (00:38:00)
Revealing mistake: In the scene close to the end when the turtles are fighting the foot soldiers on the fire escape (directly before the scene where Mikey ducks under the foot soldier's axe), Raphael thumps a foot soldier on top of his head and then rams the soldier's head into the stairwell. The only problem is the soldier's head misses the stair by about a mile. The sound effect of impact is there and the soldier even holds his head as if he were hurt. (01:17:20)
Visible crew/equipment: When Splinter throws Shredder over the wall, Splinter's puppeteer is visible. (Full screen only).
Visible crew/equipment: When Shredder is charging at Splinter with the spear the edge of the backdrop and a hanging wire are visible at the top of the screen. Full screen version.
Revealing mistake: In the scene where Raphael is thrown through April's skylight after being attacked by a few dozen members of the Foot, the other Turtles and April check on him. As Donatello and Leonardo look him over, they lean on his shell, bending it with great ease even though a turtle's shell is supposed to be almost as hard as rock.
Revealing mistake: When the Turtles make their triumphant entrance jumping in frame after the logo, at the bottom of the screen you can tell they are wearing white socks/shin guards, except Raphael who is the one the camera is focused on. (00:05:30)
Audio problem: In a close shot of Splinter holding Shredder's spear with Michelangelo's nunchaku on the building's ledge, Splinter's voice can be heard, but his mouth isn't even open (full screen version). (01:22:55)
Visible crew/equipment: After Casey takes a golf club and drives Master Tatsu into a pile of boxes, a camera lens hood is visible on the left side of the screen. It can be seen again in a later shot right before Casey and Danny carry Splinter away (full screen version). (01:14:40 - 01:15:50)
Visible crew/equipment: At the end where all of the turtles are complimenting themselves, Splinter's puppeteer is visible when he walks onscreen to say "Cowabunga" (full screen version). (01:27:00)
Other mistake: After Michaelangelo hums to agree with Donatello's comment moments after Casey & April have finished arguing and slamming doors, you can hear Michaelangelo humming "Old MacDonald," but you can see a shoulder strap and a purple headband indicating this is Donatello. (00:52:15)
Revealing mistake: A lot of times in the movie, when the turtles' mouths are wide open, you can see the cast. An example of this is the scene when Raphael wakes up in the bath tub and Leo hugs him. When Donatello tilts his head back and laughs you can see eyes, a nose, and a mouth within the mouth of the costume.
Revealing mistake: Michelangelo dodges the axe a Foot clan member swings at him by hiding his head into the shell. When he knocks his assailant out with a backhand, you can see a large gap between the mask and the rest of the suit. (01:17:30)
Continuity mistake: Two shots after introducing himself to Raphael, Casey Jones' hockey mask vanishes from its spot on the grass in the background (full screen version). (00:12:15)
Factual error: When the police chief is looking at Danny's police file just before calling his father, you can see a few different phone numbers listed. These numbers are all using 213 as the area code which is for Los Angeles, CA. Given that the film takes place in New York City and that the addresses listed on the same police file are NYC addresses, the phone numbers should be using 212 area codes. (00:28:22)
Revealing mistake: When Michelangelo and the foot soldier are having their nunchaku duel, you can see the foot soldier's weapon is foam padded so as not to injure the performer.
Answer: Most likely to kill Shredder and make sure that there would be no way to come back but, as seen in the sequel, Shredder does return.