In version 4.4.12 and the previous versions, Pix4Dmapper was rejecting negative K2 values from Micasense altum (radiometric calibration coefficients, you can read more here: https://support.micasense.comhttps://support.pix4d.com/hc/en-us/articles/115000351194-RedEdge-Camera-Radiometric-Calibration-Model) due to which the reflectance values were not being calculated correctly and the NDVI map had negative values. The bug has been fixed in version 4.5 (it is a preview version). You can download it from here.
We also had a recent data set deliver some negative values. While this was just for testing and done well into vegetation senescence, could the time of year caused this? We are using 4.5.2
Senescence could definitely cause this. Are the NDVI values still ranging from -1 to +1?
Yes, thank you for confirming these results. Nicely enough we were able to still utilize the outputs.