Okay a little background first. Playing on the Xbox One. I'm trying to get all the achievements in 2 different saves. So I went through the Brotherhood questline already. Then, in another save I'm doing the Railroad and the Institute at the same time. I just finished the Rockets' Red Glare, where you destroy the Brotherhood. Now I'm doing End of the Line where you destroy the Railroad.

I have a save a few minutes before starting this quest. Every time I play the quest there's a waypoint that I can't get to.

So, this is what I've been doing. I kill everyone in the Railroad then there is a waypoint in a random part of the wasteland. I go to the waypoint and it's Deacon walking (sometimes underwater). Then there is a waypoint back at the Railroad HQ that is just a corner in the back room.

I think what's happening is Deacon is walking back from the Boston Airport from the last mission. I kill him before he gets back to the Railroad HQ. And since I didn't kill him on the Railroad HQ cell, the waypoint is directed me to the start position of Deacon, who isn't there. That's just my theory based on how previous games with this game engine have worked.