This peculiar situation can occur in the computation of the proportion of synonymous (or nonsynonymous) substitutions per site, especially when the number of included codons is small. If you wish to know which pair(s) of sequences has this problem, please use the Distances|Pairwise option. All such pairs will be shown in the Distance Matrix Dialog with a red n/c.
The Kimura (1980) distance correction is used in a number of operations, including calculating nucleotide distances and synonymous and nonsynonymous substitution distances. These formulas cannot be applied if the argument in the logarithm approaches zero or becomes negative. If you see this error message, then this has happened for one or more pairs in your data. If you wish to know which pair(s), use the Distances|Pairwise option. All such pairs will be shown in the Distance Matrix Dialog with a red n/c.