Hello Torben,
Coordinate system axis are not shown on the screenshot, but if Z axis is inverted (pointing under the ground) then the most likely reason of the issue is swapped X and Y columns for the GCPs. To fix it re-load the coordinates for markers and use proper order of Northing/Easting columns, then press Update button on the Reference pane. In case it fixes the axis orientation, then you should re-build DEM and Orthomosaic.