Continuity mistake: As Casey draws his cricket bat, his bag is empty. A moment later, as he runs off, he has all of his weapons back.
Continuity mistake: In the first meeting with Casey Jones, Raphael jumps over Jones. As he does, Jones starts to turn around. As Raphael lands, Jones is starting to turn around again.
Continuity mistake: When Danny is admiring April's turtle sketches, he asks if he can keep one of them. His right hand holds onto a sketch of Leo at first, but in the following shot his right hand isn't gripping the sketch at all. Instead, he's seen reaching out to pick it up from the couch. (01:04:35)
Continuity mistake: When Leonardo engages Shredder on the roof-top, there is a scene where Shredder is seen close front. In that instance he is actually fighting Raphael; on the right you can see his red mask, and the weapons Shredder parries are sai, not swords.
Continuity mistake: When Shredder unbalances Donatello in the fight his left foot is close but not inside the large shadow area, but Michelangelo attacks him right away and despite his lack of movement, now that foot is in the shadow cone. (01:20:20)
Continuity mistake: The Turtles are making fun of The Shredder's name once he announced it. Look at Michelangelo when he recites the coleslaw joke; his bandanna goes down the right side of his back, but it's on the left side in the next shot. (01:19:05)
Continuity mistake: When the Turtles strike a pose after they wasted all the Foot soldiers before their big showdown with The Shredder, the ninja lie unconscious at their feet in different position. Even the roof is lit differently. (01:18:20)
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 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: 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: 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: 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: 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: 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: 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)
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.