I noticed in one episode in Season 1, the turtles drive to a place that looks like the World Trade Center, only they call it the "Global Trade Center." Then in an episode of Season 2, the turtles are flying in their blimp to the "World Trade Center" to find Shredder.
shareCould have had something to do with needing permission to use the name. It's also possible that they substituted the name for the first reference so their universe's New York wouldn't be the same as the real New York and then they just forgot about it or didn't care when the second reference happened.
Michael Bay didn't ruin my childhood. My childhood happened more than twenty-five years ago.