When you use Application Links to link JIRA and Confluence, the user-accounts and user-permissions between the applications are synchronized. If you have permission to see it in JIRA, you will have permission to see it from JIRA, within Confluence.
It sounds like you have some people licensed as JIRA-only users and some users licensed as Confluence-only users. Unfortunately, if they do not have access to JIRA, they cannot pull live reports in Confluence FROM JIRA, unless it's publicly accessible.
Can you specify what reports you are trying to use? I might be able to be more definitive.
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