1.) The first problem I encountered was with the Restoring Hope quest. I had completed this without problems with a previous character but this run after completing the quests for the Doctor, Quartermaster, and Morale Officer I am told to talk to Captain Polanski yet he doesn't let me progress to the invasion portion. I went ahead and eliminated Dead Seas anyways and the quest hasn't failed or anything... it just sits in my log.
I'm not sure what could have caused it besides that I had already completed some other quests such as speaking to Ambassador Crocker and getting the 1st Recon sniper team to move to Camp Forlorn. There were also Veteran Rangers and Heavy Troopers stationed at the base when I attempted the quest this time.
2.) The NCR Correctional Facility. On this quest I helped Eddie until the branch where I could contact Lt. Hayes and instead help him to retake the facility. I offered my assistance, talked to his go-to guy, and when he told me to kill Eddie I went after the big man. Killed him, talked to the soldier again, and he thanked me for wiping the Powder Gangers out. Great! Or so I thought... while listening to the New Vegas Radio I hear Mr. New Vegas claim that the recent attack on the facility was a FAILURE. This was my first major disappointment since the best part of Fallout stories imo is how we can shape the story. If a bug caused my efforts to be for naught I'd have been better off wiping out the facility without the quest.
3.) At Camp McCarran I'm attempting the Put A Spell On You quest but there doesn't seem any way to progress. I camped out the tower and haven't noticed a single person entering... although there was a NPC signal on my radar who remained outside the tower's playable area. I'm not sure if I'm doing something wrong but that doesn't seem like it should be happening. The only indication of who was responsible was Curtis who was walking back from the Airport entrance despite not appearing in the Airport or Tower. I pickpocketed him and did find evidence that he could be responsible but nobody I talked to seemed to have an option for progressing this quest further.
And Colonel Hsu continues to act as if I had just met him despite several conversations and missions accomplished...
4.) Also at Camp McCarran but I returned the body of Morales and talked to his wife. Soldiers still remark that his body remains in the hands of Fiends.
5.) Only somewhat related to NCR, but while doing the quest to convince the Great Khans to abandon their alliance to Caesar people began talking as though I had WIPED OUT the Khans. This caused me a bit of confusion as I was still working with Jack and Diane.
Much later when I began doing the Hoover Dam quests I was told to deal with the Khans. I talked to her again immediately after she gave me the quest and I was able to tell her I killed them all... despite being Idolized and still working on the Alliance quest. I guess I've redefined the word butcher?
6.) I negotiated with Jessup and let him return to Red Valley. However, when I found him in camp he still talks as if he's making a journey and gives no real options besides the one I had when he left Boulder City.
7.) For the Alliance quest, I've already helped Melissa recover her drugs and she owes me a favor, but when I got the quest to break Caesar's alliance I went looking for her and the quest marker only points to her camp where she's nowhere to be found. Is this a bug or am I missing something?