So anyone knows how to fix this and remove the subordinates arrow form the manager box in addition to render the manager box among the rest of boxes on the same level?
I am already using the filtration section and the filtered employees became hidden correctly but their manager is still appearing in separate column and with the drilldown arrow as marked in red above.
The only difference between my case and your elaboration is that my employee is in level 3 however in your case it was level 2, but I am not sure if this is the root cause.
P.S.: I am using SharePoint 2016 and reading org structure from the User Profile Service.
I have turned to a developer and he clarified that the issue occurs only with user profiles set as data source. We will fix the bug and I shall notify you about it. But after fixing you will need to update the Org Chart and for that it's necessary to have an active maintenance subscription.
Hello! Unfortunately, it turned out that solving of the issue requires significant changes in the code of the app. We are working on this right now but I can't tell you a definite due date when it's done. I will keep you posted with any updates I get.