The Brotherhood quest to return the lost pistol is the same for me. I brought it back and turned it in and she gave me the items for the quest reward. However, next time I talked to her, she asked me if I found it. The only option is no. Hit that option and she quits the convo. This means I can no longer buy Brotherhood items anymore. No fixing my power armor. The sweet thing about power armor, it doesn't seem to be factional despite being the staple of Brotherhood identity. NCR has power suits, but they svck. Aside from that, there aren't enough of them out there to repair your Tbd-85 armor; the best armor in the game as far as I've seen. So, I guess after my armor is broken, I have to drop it or kill the Brotherhood and store their armor because I will never be able to buy replacements.
On other quests, I've had several where having a companion means I can't finish. I took Raul with me into a few faction places just fine. If I did a quest and returned, they would automatically attack him. This hasn't happened with any other companion that I've seen, but it happens with Raul all the time. Everybody seems to hate him when they see him a second time.
The Tabbatha quest at Black Mountain can become unplayable sometimes. I've had her quit conversation twice and start attacking me. Even more funny though is that after you finish the quest. If you run down the mountain and then come back up, her guards will not recognize you anymore and immediately start attacking you. Stupid Nightkin.
One Ceasar Legion quest I've been doing seems to abruptly stop before I can finish it. When I'm heading to the Boomers, so far, I have only made it to the perimeter before the guy starts talking to me at the gate and then it says quest failed. Dunno why. The NCR version never failed me for running up to the gate.
I uninstalled my Classic Pack and have gained quite a bit of stability. Freezes less often. However, the falling through the ground thing happens a lot more now. Another Raul problem I have is him falling through the ground and getting stuck. I'm sure it would happen with other companions, but he's the only one I've actually witnessed this with. He'll fall in, once you walk over where he fell in, you'll hear him saying his dialouge when you get close. Yet, you can't click him, bring up the wheel, or anything. He's just stuck there. I've fast travelled away and came back to find him still in the same spot, so he doesn't warp with you in that instance. Not sure what the deal is.
Just a few problems I've had........constantly. Hopefully these will help if Beth or Obsidian is actually viewing these.