@James, you can upload the quality report here and we will have a closer look. Please also specify where in the quality report can we see the problem.
As for the vertical coordinate system, it is not possible to import vertical coordinate systems. There is, however, a way to introduce a shift in the vertical coordinate system.
To introduce this offset in the software, you can use the Geoid Height above the Ellipsoid function (which simply introduces a vertical offset). You can find out more here https://vdatum.noaa.gov/docs/datums.html, which also offers a tool to compute this offset depending on your location.
We also have a video on this topic: Altitude and Vertical Coordinate System - Pix4D Video Academy 14
@Levi,
Could you give more information about the project you are processing? What are the coordinates system that you use? Could you please upload the quality report here?