A Google Maps Help thread has a bug report from two different iOS users with the transit directions in the new Google Maps app.
In short, sometime the transit directions are right and sometimes they are wrong. It depends on which device you are running.
An iOS developer said he has two iPhone 5 devices, both running the latest stable release of iOS 6, i.e. 6.1.4, but in one, he gets wrong transit directions on the Google Maps app and the other he gets the correct transit directions. He has no idea why.
He even posted screen shots:
Google's Daniel said he'd pass this along to the team but there has been no word since he left this response:
Thanks both! I'm duplicating the other thread Natalie started to this one. I'll also send this along to the team!
I am not sure what priority this is for Google and the number of people using transit directions on iOS but it does seem to be an issue.
Forum discussion at Google Maps Help.