So I just had this happen to me, where I killed The Lamb, but the game didn't give me the Lamb Wisp for the Special ending. What it did do was trap me in the final room where the grave is instead, so I had to figure out a solution to get it to work. If the special ending doesn't trigger, it is most likely because one of the wisps didn't spawn in properly. What I had to do, in my scenario, was simply enable the Debug console through the Options.ini in the game files, and then simply use the spawn command to respawn the Lamb, which instantly fixed it and allowed for the mod to progress to the final stage in which the unique ending happens.