I'm having what sounds like the same issue, although not arising from a Jira import.
The Relationship Status column of my Requirements Set shows a Missing Downstream flag against each requirement (see top screenshot). A randomly selected requirement, when opened, shows 1 up (grey) /1 down (red) on the Relationship Status Indicator, and lists both upstream and downstream items in the Relationships pane (see bottom screenshot).
Only the Requirements with "not applicable" in the Verification Method column should show no downstream relationships (they contain design guidance or definitions referred to elsewhere in the Set).
There are no Suspect Links in the project.


Edited to add screenshot showing mouseover text: