I am having the same issue but I'm playing on PlayStation 5. It's one of the final two trophies I need to platinum. Like you I've experienced no issues interacting with the altars in my first playthrough but when I came to "mop up", I've noticed that the altars do not register as triggered - the same number of triggered altars appears after I've gone through a guide and triggered all in the area.
I was beginning to think I was alone in this. If others like yourself are experiencing this too, hopefully a fix will be applied in the future.
