I don´t if it´s a bug or what but suddenly my PBI Desktop shows these weird overlapping object selections in the right pane.
My file is about 55,000kb and it has 1 filled map, about 3 tables, 5 slicers, and 5 chart visuals plus some images.
I have made a test but couldn't reproduce your issue. The layer order pane works normally on my side. My desktop version is 2.82.5858.1161 64-bit (June 2020). Please update power bi desktop to the latest version and check again. If this issue persists, I would suggest you create a support ticket here for further analysis.