The orphan issue occurs when you use the Create/Select dialog from ClearQuest to link a record and JIRA issue and are not logged in to a JIRA web session.
When you start the dialog from the Links section of a ClearQuest record, you are prompted to log in to JIRA. However, the JIRA login does not take effect and no link is created after you click Submit. If you also specified to create a JIRA issue, it is created, but not linked to the ClearQuest record.