So I did all the side quest that I could before going to Benny (about 50 hours of game play). I have talked to Mr. House also. So I go to start the Benny and guessing end-game quests. I noticed in a forum that afterwards you get confronted by a Legion rep and a note from the NCR. I want to follow the NCR, but never got the note. I did get approached by the Legion guy.

Has anybody else run into this problem/glitch or am I doing something wrong?

You get the NCR note before you deal with Benny. Like, right after you talk to House and get your room at the 38.

Your faction standing may have some effect on this. I was terribly hated by the Legion my first game so I never got a Legion representative. You may also not get it if you start doing quests for Crocker beforehand, as that would be redundant.

I read something about a mission with him where you kill the King, which I helped and a member of. Maybe that's why I didn't get the note. I looked through all of mine and there is nothing about going to him in the embassy. The one thing I love about Fallout, too many side quests that interfere with the short main story.