I just finished this quest last night without issue (1.3). Thankfully none of my thieves guild or companions quests have had any bad bugs like this. But I do have an issue with this quest line that I want to get off my chest.
All I wanted was to free Kodlak and then cure myself (because up to this point I didn't particularly enjoy this quest line or being a werewolf). I thought this is where it would happen, but I didn't get the option to cure myself. Upon leaving I went to Windhelm to do my usual vendor run, where I sold the witch heads just to get them out of my inventory because OCD. Then upon sleeping I noticed I still had beast blood. Decided to quit to desktop (had accidentally closed the Task Manager tab earlier, so I couldn't tab out to desktop) and look on uespwiki to find out what was going on. After reading about what to do, I had run back to Windhelm to retrieve my witch heads, then back to Jorrvaskr to get the quest from Farkas, then back to the tomb to kill his wolf spirit and hopefully mine too so I could just be done with the werewolf crap. BUT NO! I was still FORCED to go back to Jorrvaskr and do the same damn thing for Vilkas before I could rid myself of this crap. Sigh.
Should have given me the option to cure myself when I was sitting there the first time with Kodlak. I can't imagine how [censored] this was for people who don't fast travel.
Anyway, back to your quest-breaking bug.
