I know that TMNT is considered to be the fourth film, but there is evidence proving that it is actually a separate continuity from the live-action trilogy.

One is that Kevin Munroe himself stated that the events of the live-action films DID happen, but not in exactly the same way.

The other evidence I've noticed is that Splinter has both of his ears intact, while Oroku Saki cut one of his ears off in the original films. The 2007 film's Turtles were even shown to be separate from the early 90's movie Turtles in the multiverse scene in Turtles Forever.

If anyone disagrees with my observations, please explain to me why you believe that the CGI film is canon to the first three films.