However, what kind of case could MBTA possibly have against some kids who found problems with their infrastructure?
The flaws they found allowed them to obtain, according to their talk's description, "free subway rides for life", which would deprive MBTA of an unknown amount of revenue which was rightfully theirs. They wouldn't disclose the vulnerability when MBTA approached them, although they changed the description of the talk to no longer imply they would explain how to get free rides.
You can read the MBTA complaint yourself: http://www.universalhub.com/images/2008/mbtamit.pdf