This is the third time that it's happened.

First it was the door leading into the Railroad meeting which I circumvented by using TCL and going up to the roof to enter it from there (I had entered this location through the main door at the bottom previously but decided to go do another quest before I wanted to start up the Railroad quest).

Then it was a door I can't really remember.

This time it's the big building at University Point which I can't enter from either of the two entrances.

What happens is that the "click E to open door" prompt doesn't show up and if you go into the door it's like it isn't loaded. Like, it's there, I can clearly see the door, but I can walk through it.

How do I fix this? Can it be fixed?

I've also had this issue from time to time. The only door I almost always have problems with is the door into the main Railroad area, as you've mentioned. On both sides of that door it can be problematic to find the door activator. From memory it has happened on one other door for me, but unfortunately I can't remember where it was.

I've stopped playing the game for now as I'm waiting for the GECK to be released as I'm keen to start modding my game, but yeah, I can say that the Railroad door activator definately has issues.

At the latest door I had an issue with, University Point, I saved in front of the door (just beyond reach of activating it), quit the game, started it up again and the door worked again.

So, yeah.

I guess that's a solution?