The JIRA integration can show 0% progress even if some tickets that the JQL returns are marked as complete if it is an epic and the JQL entered in Ally is of the form:
issue = AI-20
"Epic Link" = AI-20
cf = AI-20
In order to resolve this, enter the JQL as "Parent Link" = AI-20 in the JQL field of the JIRA Integration setup in Ally.