I started the Show No Mercy mission (first mission for Brotherhood of Steel once you operate off the airship) and found 2 bugs, one minor, one HUGE.

MINOR BUG: The objective marker when on the Prydwen (spelling?) leads to the transport down to the airport; once you get to the airport, it just shows you should get back on the transport and go back up to the ship, until you've moved a fair distance from the landing pad.

MAJOR BUG: Appeared when I got to the beach, where I should have been able to board an armed V-bird, according to the online walkthrough I finally turned to. But in my case, what I found was an objective marker hovering about 20 feet in mid-air, and (believe it or not) a pilot up to her neck in the water. The bird itself was parked 20 yards away or so down the beach, where it gave no prompts to board. I couldn't even jump on. Eventually I just walked to the rest of the mission.

I saved, quit, restarted from old save points, and reloaded the game 6+ times, getting the same result every time.

Maybe there will be a patch by the time I start another character and get back to this point (I'm thinking I might run a female through, just for variety next time...).

I'm interested to know if anyone else has experienced this, and if it existed pre-patch or has come up since the recent patch.