Continuity mistake: When the turtles are fighting Shredder, in the second go-round so to speak, the order is Donatello, Michelangelo, Raphael, and finally Leonardo. When Leo is knocked to the ground, the next shot shows him leaning over the edge of the building as Donatello walks into shot holding his shoulder as if he just did battle.
Continuity mistake: When Raphael knocks down Casey Jones and enables the purse snatchers to escape, they are getting up off the ground and running away. In the next shot, they are again seen getting up off the ground and running away.
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: 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: 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)
Other mistake: The clock behind the couch April rests on (and crawls terrified on when she wakes up) indicates 5:35 for much longer than a minute. (00:21:30 - 00:23:00)
Audio problem: In the Italian dub, Chief Sterns reads Mr. Pennington's number as 555-5219 instead of 555-5214. (00:28:30)
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)
Revealing mistake: In the opening of the movie, a citizen is reading his copy of the New York Post and you can actually read the date; Wednesday September 12, 1990. It is obviously a movie prop though, because the scene was shot in late 1989. How can you tell? Easy; he is reading it next to a newsstand kiosk full of magazines from that period; instantly recognizable are Vanity Fair's November 1989 issue with Baryshnikov on the cover, and GQ from December 1989 with Sting sporting an epic 'stache. (00:00:50)
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)
Continuity mistake: During the fight in April's apartment, The Foot Clan member swings his weapon at Donatello and misses knocking out the power as seen by sparks which causes the fire. Somehow April's answering machine still works, though.
Continuity mistake: When Raphael angrily leaves and practices his Ninja moves on the roof, he appears on a white building. When he is thrown through the roof down to the other Turtles, it is still a white building. The building in which the Turtles fight The Foot and catches fire is the "Second Time Around Antiques and More" shop where April lives which is brick, not white.
Other mistake: After Leo's failed attempt of fighting Shredder for the first time, Mikey and Donnie then play Rock, Paper, Scissors to see who fights Shredder next. It then cuts to Casey talking to "The Foot" where you can hear Mikey fighting Shredder. The next scene shows all four Turtles in a huddle regrouping, breathing heavy, and out of breath. According to what we heard, Donatello shouldn't be out of breath as he has not fought Shredder for the first time yet.
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 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.
Visible crew/equipment: In the rooftop fight sequence with the turtles and Shredder, Raphael jumps over Shredder's head at one point and, here, you can see the crash pad that he lands on (full screen version). (01:20:05)
Visible crew/equipment: When Leonardo takes his first turn attacking Shredder on the rooftop, you can see the raised platform that he leaps from, which gives the effect of a very high jump (full screen version). (01:18:55)
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.
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.