What sort of data are you trying to process?
Did you first calibrate the data to either TOA reflectance or surface reflectance prior to calculating the VIs?
The VI Calculator will use a biophysical cross-check to make sure the output values are valid. Additionally there is another mask applied to out of range values. I wonder if you might be running into this issue:
http://www.harrisgeospatial.com/Learn...
https://www.harrisgeospatial.com/docs...