System Xbox 360:
Build Version:
1.3.0.444

Though this also occurred with an earlier build.

After completing Bitter Springs, I returned my character to the hotel room in Novac. Unloaded all the excess equipment and set him to 12 hour sleep.
I was awoken at 2 hours remaining with a great khan standing at the bottom of the bed. As I went to exit the room a Powder Ganger spawned inside the room, then followed me outside where Boone killed him. No surprise there.

This had happened before, on an earlier build, I restart from the beginning though with each patch update.
The last time it happened it was in the Lucky 38 and all my NPC characters I had collected vanished and were replaced with Great Khans wandering around the Lucky 38.

Also I have found if I dismiss Boone and he goes back to Novac he will randomly appear while wandering through area's and ask if its time to rejoin the group.