This question is in reference to Atlassian Documentation: Configuring Swimlanes
On y scrum board, when using 'Base Swimlanes on Epics', the Sub-Tasks that are directly under Epics are shown under 'Issues without Epics'. How can I make it show under the Epic it has been created for?
Nic's correct, note the message on the Edit screen of a sub-Task;
Since a sub-task can not be assigned to an EPIC, you get the very results you have identified. Yes, the EPIC is the parent issue, but JIRA does not see the Parent as an EPIC because of the notice above.
Use Nick's solution to resolve this problem.
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