Hi! I had this issue in my game as well, and came across your post in my search for a solution.
I'm not sure if what happened with me was part of the issue but I had the hidden treasure quest and Last RItes active at the same time. My solution was to reload to a save before I even activated/accepted the Last Rites quest. I then did the other surrounding quests in Dock Town, cleared those out before interacting with the note about the Venatori to activate Last Rites.
When I did get the quest active (with no others active at the same time), it seemed to have loaded the crystal walls/barriers correctly (they did not appear for me at all the first time, just the floating red crystals) and I was able to destroy the crystals to access the note beside the body at the ritual site.
I don't know if what worked for me will help you or anyone else with this problem, but hopefully it does, as I found it veryyy frustrating to deal with myself;; and I couldn't bring myself to ignore it;;
Hi, just wanted to let you guys now that I'd also been dealing with this bug on PC, but the patch released today has fixed it!
