Issues are not being synchronized when an issue has multiple associations with both autopush and autopull enabled.
When a user updates a Salesforce record with an association, the record will be synchronized to Jira automatically.
Once the Jira issue is updated by the Connector, it will trigger an auto-push event to push the changes to all associated records, but this action will not actually be performed.
Most likely the integration user is not a Jira user account that is dedicated for this purpose.
The Jira admin must create a dedicated Jira user for an integration user to avoid further synchronization problems.