In ARCGIS Pro, when creating layouts some layers appear duplicated in the legend. When I try to remove one of the duplicates both instances are removed. Additionally, some of the layers cannot be turned off individually. The only way to remove these layers is by deleting them.
This is a BUG. There is another ArcGIS Pro question referenced here that discusses this bug quite a bit as well as various resolutions based upon ArcGIS Pro releases. What release of ArcGIS Pro are you currently using?