Hi jazzyj,
If you took off near sea level, there won't be any problem
If not, there are three things you could do to fix the problem:
1. Change the camera accuracy to a large value in the Reference settings
2. Uncheck all photos in the reference pane, which means only your GCPs will be used
3. Change the XMP/EXIF information of your pictures by adding the elevation of your point of take off to your flight height (point of take-off = 0m for DJI drones). This can be done with a Python script or with external software packages (e.g., ExifTool).
Regards
SAV