Hi @AlfalfaResearcher, thanks for reporting this problem.
The problem here is that the matrices you are trying to fit don't have the same dimensions. This would usually happen if one or more of the samples were dropped out during rarefaction or weren't processed with both primer sets. If this is the case, then you could make the matrices comparable by filtering them to include the same samples, see qiime diversity filter-distance-matrix.
The error message is confusing, I've fixed this in the code so it should be clearer for the next release 
.