I believe this is a JIRA bug.
I was filtering on component, and items were not showing up. My filter contained "component not in (thing1, thing2)". I have many items which component is not set (EMPTY). I finally was able to solve this issue with (component is EMPTY or component not in (thing1, thing2)). JQL should not filter out EMPTY when component not in is being used which is what I think is happening.