Approval of God: Kevin Eastman, who, outside of the Creator Cameo in the end, was not involved with the making of this film, admitted that this was one of his favorite TMNT films.
Deleted Scene: Apparently there were plans for a scene in which Rocksteady finally got to use his machete, but they cut it for some reason.
Edited for Syndication: Some scenes (or parts of scenes) were edited out of the broadcast version to make room for commercials, and it's fairly apparent at times. For instance, there was a scene that explains how Karai had tracked Ch'rell to the Technodrome, and another scene that gets an emotional Call-Back in 1987 Splinter's scene.
Exiled from Continuity: It didn't go unnoticed that the montage of dimensions didn't include Ninja Turtles: The Next Mutation. This is often attributed to Peter Laird's extreme dislike of the character of Venus, though it should also be noted that the rights to that show were tied up anyway due to Saban Entertainment having their various properties bought by Disney several years earlier, though it's quite likely Laird's dislike meant there was no incentive to get the legal issues sorted out anyway, and Saban has since bought it back. The rights currently rest in Hasbro's hands.
Fandom Nod: Some of the more irate comic fans believed that Eastman and Laird sold out the TMNT by "kiddifying" them for animation back then. Here, Mirage Raphael calls all of his counterparts "sellouts".
No Export for You: Possibly due to the fact having to replace the entire cast of two different series, not to mention other problems, it's very possibly this film will never be shown outside the U.S. It was released in Canada and the United Kingdom.
that explains how Karai had tracked Ch'rell to the Technodrome, and another scene