This is NOT the fast travel entrances in Boston and New York. Those are #10 and #11 locations respectfully. I searched and searched; the game and the Internet- No joy. Then, while liberating a fort(?) in Boston, a chest and several enemies (red markers) were showing on the mini-map, and yet there were none to be seen... so I went over the wall just adjacent to where those were showing on the map and dropped down to small roof, covering a door. After going inside that door, I found the enemies and the chest. Upon opening the large map- then the log, I found that the "Discover 5 Underground Network Entrance Locations" was now 1/5. Soooo, THIS is evidently ONE of the hidden entrances that nobody can seem to find. I do not know if all of the entrances are under forts. (I have not yet traveled to New York.)
RonRay