After updating Apps with new reports these reports do not show data in the usage metrics. Only the original (and first) report published at an earlier date. So I currently have 4 reports in my App and I see only 1 in the Usage Metrics, however I know (and I see them in my O365 audit log) that users are looking at the other reports as well.
The only Usage Metrics that seem to be recorded for the 3 new reports are the ones where you directly open the report in the workspace (and not via the App). However almost all users only have access via the App.