In the original script, the film was to end on a cliffhanger, with Prof. Perry being revealed to be a robotic shell for an utrom, aliens from the original Teenage Mutant Ninja Turtles comics who created the ooze to power their technology. This was dropped due to the fear of kids mistaking it for Krang, a villain of the cartoon series who was based on the utroms.
When Shredder raises his hand out of the dock that has collapsed on him at the end, it eventually falls limp indicating he is dead. However, the spikes on his wrist shake, indicating that they are in fact rubber.
When Keno is waiting outside for the Foot audition, a certain part of Manhattan is visible in the background, however, when he is walking into the building, the background shows that he is at least a mile away.
What are the differences between the old British VHS and the uncut British DVD?
Due to the usage of martial arts weapons two scenes in the old British VHS were cut. These cuts were waived for the DVD release of the movie. Nonetheless a detailed comparison between both version with pictures can be found here.