I'm currently having a bug in ArcGIS Pro 2.5 (though this also happened in 2.4.2).
When georeferencing a TIFF file, with or without Auto Apply enabled, when I go to save the control points/georeferencing session after adding new control points, the map disappears and all control points are lost. If I then repeat the georeferencing, once I click save again, the points "stick" and the Tiff is then georeferenced. Thoughts? My colleagues are having this same issue.