Why are there chromaticity values of zero or less than zero in the Munsell data on the MCSL web site?
There are such values in the file all.dat. As explained on the Munsell renotation data page, this will contains unreal colors. That is, colors whose chromaticity coordinates lie outside the Macadam limits. One such color: 2.5PB 0.2/20 is shown at the lower end of the red line in the diagram below. The unreal colors are only useful if you want to interpolate color that lie very close to the Macadam Limits. Note that for this very dark color, value=0.2, the spectrum locus is essentially the same locus as the Macadam Limits at this value.