Meanwhile, the rest of the game continues normally (that is, I'm defenseless and getting torn up). It doesn't happen often, nor when I reload outside combat, but the couple times it has I was generally fighting strong enemies like Cazadors or Legion Assassins, so it was a little more than just inconvenient.
Movement and looking is unaffected. Can't remember if the Pipboy is able to be used or not; if it happens again, I'll try it and update this post with definitive results. Update: Pipboy doesn't work, either. Seems to occur exclusively with sing;e-round loading rifles (Cowboy Repeater, Trail Carbine, Hunting Shotgun, etc).
Companion Bug: Sometimes, my companion (Boone) simply disappears during loading screens. Memorable times include exiting the Tops Casino after meeting with Benny and after being taken to and from the basemant of the Lucky 38. It doesn't happen often, but when it does it requires me to load a previous save, which is... inconvenient, since I'm not too good at saving constantly.
In one area, Boone, in fact, refused to follow me through a certain door (the cellar door of Brewer's Beer Bootlegging). Meaning, I left the room, noticed Boone was not with me, returned to the cellar and found him there.
This is from pre-patch, so it may have been fixed. I hope this is the case, but wanted to mention specific instances for the sake of thoroughness.
Legion Bug: After being given the Mark of Caesar and traveling to Cottonwood Cove, I was immediately set upon by the Legion, without provocation. Contributing factors might have been: I killed Vulpes Inculta in Nipton (hey, he basically told me to); completed Restoring Hope, earning a "Vilified" Legion reputation in the process, and had Boone as my companion. If Boone really is a factor to Caesar's Legion attacking on sight (as a forum post suggested it might be), it would be nice to mention that in-game, since I ended up fighting through The Fort to a certain weather station.