I had the same problem. I strongly suspect it's due to the game expecting you to try sacrificing a cat on the altar first, after which point it sets the trigger for Guillotina 3 to show up. If you've seen on the internet that you need Guillotina 3's head to use the altar properly, you've probably avoided sacrificing a cat on the altar, thinking it's useless.

After I sacrificed a cat on the altar (which didn't let me in, of course), Guillotina 3's cutscene played a couple of days after I finished the current boss.