Hi Sean,
Well, each time our custom post types are registered (which occurs on every single request, as is the norm) we also add various additional capabilities to a number of default roles.
So, depending on how your capability editors are working it’s quite possible this is stopping you from removing capabilities even if it doesn’t prevent you from adding capabilities.
I’ll certainly raise this as something for us to discuss and potentially reconsider and update you from there 🙂