Continuity mistake: At the beginning of the movie, the stolen wallet ends up in Danny Pennington's hand who is tasked to hold it out for the ninja to grab it. In close-up Danny's hand is positioned below the sleeve of his T-shirt, in the shots before and after his hand is higher, between the sleeve and his body. (00:01:15)
Continuity mistake: In the beginning, after the Turtles save April, you see her jacket is on correctly as she sits up. A second later, it's off her shoulders. (00:04:25)
Continuity mistake: As he shouts down to Michelangelo through the sidewalk grate, watch how the pizza man's $10 bill changes from left hand to right in between shots. (00:10:20)
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)
Continuity mistake: After decking Raphael for the Jose Canseco remark, Casey's baseball bat instantly changes hands between shots. (00:12:35)
Continuity mistake: When April tries to rationalize what she's seeing, says pointing at the Turtles; "And you guys.. " Mike and Leo are looking at her. Leo's arms are low, but in the reverse shot they are held higher towards her. (00:22:25)
Continuity mistake: When April naively asks "You guys like pizza?" in front of the manhole, her hand drops in the close-up but is still up and pointing in the wider angle. (00:25:40)
Continuity mistake: April is laughing at Mike doing a Rocky impression. Camera behind her shoulder; notice her hand slips off the table. Back to a frontal view, and her hand rests on the table as it was before. (00:26:10)
Continuity mistake: While driving Danny to school, Charles' left hand grips the steering wheel. But in the following shot where Danny opens the door to run away, his left hand is resting near the window sill instead. (00:30:25)
Continuity mistake: After Master Tatsu kicks his opponent in the face, a couple of bystanders in the background instantly move further apart from each other between shots. In addition, one of them is a Foot member who loses his nunchaku as the shot changes. (00:32:30)
Continuity mistake: After Raphael has a fit and walks out of April's apartment, he goes up on the roof to vent his anger for a while. Pretty soon, Casey spots him from another rooftop several buildings away while tuning a radio. As Casey looks out at Raphael's faint image in the distance, pay close attention to the background as well as the white building Raphael is standing on (you can notice the Empire State Building among other landmarks). When Casey grabs some binoculars to take a better look, Raphael can be seen resting on a brick ledge. In the following shot Raphael looks out at the city towards Casey's vantage point, but from Raphael's position, the Empire State Building - as well as the white building where he was venting just moments before - are visible on the skyline. Somehow Raphael has managed to relocate to another building's rooftop between shots. (00:38:15)
Continuity mistake: In the rooftop fight, as Raphael quips about the Foot guys studying the abridged version of the Ninja book of fighting, you can see his belt is hanging kinda low, at the hips almost. In the next shot, Raph is fighting with his belt in senior citizen mode, pulled all the way up to 2/3 of the torso. You can tell quite easily because being a turtle his belly is divided in sections. (00:40:45)
Continuity mistake: Mike thanks to Don's help does the "Wheel of Fortune, dude!" move; the floor next to him is relatively clear from debris and he sweeps it, but when the bad guy throws a single axe strike next to his head, the floor is all messed up and cut. (00:44:00)
Continuity mistake: During a fight sequence between the Foot Clan and three of the turtles in April's apartment, keep in mind that April is still tending to an injured Raphael in the living room. But as the floor collapses into an antiques store below, you'll be able to spot her on the lower left side of the screen shielding her eyes from debris - instantly in the store before anyone else (except for Master Tatsu and several other Foot members, who were waiting there to begin with). (00:44:15)
Continuity mistake: In the rumble inside the antique store, Mike at one point squeals that they could use Raph, "right about now." Cut to Donatello fighting some bad guys to the left of an unimpressed and passive Master Tatsu. The following shot has Don fighting Foot clan members to Tatsu's right, and it's Leonardo to be battling to Tatsu's left (right side of the screen). (00:45:30)
Continuity mistake: Casey Jones arrives to the save the day. Michelangelo does a Wayne Gretzky reference. Notice in the background Master Tatsu, solitary and surrounded just by old abat-jours and other dusty curio. When he orders in his spartan English to "attack", he suddenly has a bunch of goons all over him. (00:46:05)
Continuity mistake: Master Tatsu is raging against the students, and slams one against the lockers. Another Foot soldier tries to restrain him. The unmasked victim of the assault is clutching the shoulder bit of Tatsu's hood, but his hand is further down his arm in the reverse shot. (00:49:00)
Continuity mistake: In the alphabet game of insults, Donatello calls Casey Jones "elf lips." Casey puts the monkey wrench on the radiator next to the dirty rag, but in the next shot the tool is gone from there and is in his left hand instead, so he retrieves only the rag from under the hood. (00:53:10)
Continuity mistake: Right after Donatello busts through the barn doors with an old Ford truck, its hood closes by itself between shots. (00:53:10)
Continuity mistake: Just after the Turtles train by fighting with each other, Michelangelo is in the barn punching the punching bag. The very next shot is Raphael on top of the barn shouting out Splinter's name. Upon further inspection at the weapon at his side, this is not Raphael. It is Michelangelo. (00:56:45)
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.