Using the lat/long/vertical (WGS84) from the UAS, processing through steps 1,2,3 and saving contours in NAD83 Tennessee, I get contour values that are negative. I don’t have any GCP’s for this site. NOTE: We are just getting started using Pix4D so we are still learning. Comments please…
It seems like perhaps the Vertical Coordinate System is not correct, meaning that the reference surface for the elevation (geoid height above ellipsoid vs. MSL) needs to be changed: https://support.pix4d.com/hc/en-us/articles/202560029
Make sure to select the Advanced Coordinate Options check box in order to edit these settings.
You will find more on the vertical datum here: https://support.pix4d.com/hc/en-us/articles/202559459
Let us know if this solves your issue.