So, a long time after completing the Van Graffs mission where you set up the CL in a warehouse and sell them out to the NCR, I finally got the Explorer perk. After a mad dash to find as many locations as possible for an achievement, I come across an abandoned storage area near the Allied Offices. I enter, and discover this was the warehouse I originally appeared in for the Van Graffs. Inside were the crates and the pack brahmin in the corner, and three CL soldiers standing in the middle of the room, and not hostile (despite me being Villified by the Legion, having Boone in my party, and not wearing any Legion clothing). Boone does not attack them. Running around the warehouse are 6 NCR troopers from the raid during the Van Graffs mission, not attacking the Legion at all. They keep running in circles.

So, I set up a little expirement to see what the hell was going on. I drew This Machine out, and shot a Legion member in the face. His buddies did not turn hostile, I gained experience for the kill, and no infamy was rewarded. I shot the other two and the same thing happened. I brought Boone outside, saved, and then re-entered the building. The Legion members had already respawned, still in the previous state. I did the same thing, getting free kills, experience and loot. I saved, then shot an NCR soldier in the face to see what happened. His buddies turned hostile, I did not get any experience, and I gained infamy with the NCR. So, I shot the rest, then reloaded my previous save.

Has this happened to anyone else?

I found a cave that had NCR soldier hostages guarded by CL members. Otherwise it's similar to your situation. They weren't hostile to me despite the fact that they really should have been and the Legionnaires outside the cave were indeed hostile.

I think it's a faction/hostility bug.

Im actually glad the Legion soldiers respawn. I can now farm free and easy experience, loot, and certain achievements.