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Structure pulling items not linked

Hi everyone, 

I am having an issue with the Structure feature when I try to view linked issues. 

I have a simple Jira query which pulls: issuetype = "Portfolio Epic" AND Team=44264 - >our team id.


And I use two extend generators:

- Add issues belonging to epics

- Extend with Advanced Roadmaps(Portfolio) child issue


If I look below at a specific Epic, it shows me one level below a User story which is not linked to the Epic and I am not sure why. If I click on that Epic and I go to the section below that shows me the "Issues in feature" I don't have that User story there. That particular story is linked to a separate Epic and Portfolio epic. 

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