They fixed that in the movie, though.
In a way, this isn't a fair fight--the Turtles use short-range weapons, and for all that people can't stop talking about Batman's gadgets, neither he nor the other people on his team usually use weapons. I said earlier in this thread that the Bat-people would win. What I should have said was that I think that Bat-people are better fighters. Because when you're unarmed, and your oponent has a pair of swords, you're going to have to be much better to win.