As a big fan of the animated series during my childhood, this really irked me about the movies. Now I'm grown up and my kids are watching the new 2012 animated series, of which I've seen a few, and we recently watched the new movie together.
In the animated series, Splinter's back story is that he was a human who was enemies with the Shredder. One day he was walking back from a pet shop with 4 turtles, when an accident with the mutagen caused him to be mutated into a rat-human hybrid due to interaction with a nearby rat, while the turtles were mutated into turtle-human hybrids because of their interaction with him. This is quite consistent with the new animated series.
The movies, on the other hand, have Splinter begin as a rat that is transformed into a human-rat hybrid by the mutagen (like the turtles).
Is there any official explanation for this? The movies seem a little more ludicrous to me because it's far less likely that a rat would master a martial art to the same/similar level as the Shredder, who has been a ninja his whole life, in just 18 years. And from reading books on it, no less (the first movie implies that he learned the martial art as a rat before being mutated, which is even more ludicrous).