If you've never read the comics, huge spoilers are about to come up. If you read the comics, you'd know that the turtles were mutated by ooze that was formulated by aliens under the guise of a research laboratory. That can raise questions concerning what Michael Bay said, and what that makes the turtles.
First of all, it asks, "If an alien compound is the thing that mutated them, wouldn't that make them aliens of some kind?" To answer this, I'd like to bring up District 9.
In District 9, Wikus (the main character) is infected with an alien compound and slowly starts turning into one of the "prawns" (alien creatures). Now naturally, that would make you assume that he turned into an alien. Wrong: he mutated into a prawn. He was a human; he was naturally born a human. And most importantly, he's from Earth. Technically, he's a mutant that resembles their species.
Now, with the turtles, it's a little different. They mutated from regular turtles into another humanoid species instead of resembling Utroms (the aliens that created the ooze). However, the concept remains fundamentally the same. While the ooze could be a compound that was formulated off of Earth by otherworldly creatures, since the ooze mutated Earth-born turtles, the mutated outcome cannot technically be considered "alien" in the extraterrestrial sense.
It also asks, "Keeping the origin of the ooze in mind, could Michael Bay's summary about the turtles have been poorly worded?" While the term "alien" could be used as a synonym for "strange", Michael Bay could have just been shortly elaborating that the turtles' (and by small extension, Splinter's) species is alien to life on Earth, as there are no other mutated creatures on the planet that we know of. He could have been commenting on the materials used to mutate them; as the materials were created by extraterrestrial life, so by extension, listing their species as "alien".
If it weren't for Bay's record, we probably would have assumed this. However, with his treatment of Transformers, we're ready to assume that he means they will be aliens, as in, from another planet all together: one change that would completely change the TMNT universe. And that doesn't make us (fans that have been wanting and yearning for a dark, more mature portrayal of the turtles akin to the original comic book) very happy or anticipating this movie.
We can only hope that it was poor wording on his part. And that he plans to make the turtles (and Splinter) Earth-born and mutated by ooze. Because this is one franchise where if you change one trait of the name, you just changed the whole damn franchise.