Phylogenetic error. Although switch errors in phase inference can be small, in this case 1, the phylogeny size could be significantly altered. Therefore estimates such as mutation rates could be significantly affected if performed on computationally inferred haplotypes as opposed to genotypes. Moreover, in current methods it is impossible to say if the inferred phylogeny size is larger or smaller than that of the phylogeny from the true haplotypes.
Sridhar et al. BMC Bioinformatics 2007 8:472 doi:10.1186/1471-2105-8-472