Custom Post Type + Categories

I’ve installed Custom Post Type UI plugin on my client’s site. I have registered two new post types called Resources and Case Studies. I’ve enabled them to have categories and tags support. All of this works fine.

However, I want to be able to show categories of only one custom post type in the sidebar for case studies and only the categories for the other custom post type for resource posts. Right now they appear to overlap and share categories and tags. Is there something I am missing?

If you view this page you will see the sidebar shows case studies as an option when this is a resource post. Similarly case study posts have a link to resources. I want the categories to be separate.

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