Maya Render Layer Bug
I’m sure you’ve had this, multiple render layers, different shaders on each. Eventually, it will break. Especially if you’re assigning materials on a per-face basis.
It’s better to not do that. But, whenever you have a scene that breaks and your renders are unpredictable, you can use this to fix it.
Run that MEL command. That should fix some of the errors. Sometimes, it will revert whenever you save and close the file, but you can run it again whenever you open the scene again.