Unfortunately I'm afraid the bug is not gone completely. I just finished a run where it happened again. I'm not sure what happened exactly and to be honest I'm not keen on trying again. In short, I wanted to check how the end fight looks when I ignore all optionals. I entered on elite on a sorc 20, and zerged past everything while invisible, killed the few mobs needed to drop the barrier, rested at the last shrine and dropped down to the end fight. I had red dungeon alert at the time and during the end fight it was mostly red and only sometimes orange. I fought the mobs mostly just dropping firewalls everywhere and jumping around sometimes invisible to avoid a bit of aggro. I did the 1st puzzle myself and I think the 2nd one (not sure if I finished it or one of the mobs stepped somewhere and finished) but next one was probably completely done by the mobs running all over the place and at some point the puzzle bugged. Below is the screenshot shortly after I noticed it. I believe I was fighting last medusa at the time and the hag was active.
Here is how it looked after the hag went away and I killed most of the spawns. I was ready to complete last puzzle (the quest finished when I completed it, I didn't have to redo the buggy ones). Extra chest for killing medusas appeared a bit earlier.