I believe I have discovered numerous errors in the NA12878 dataset. We are working with the most recent version,
NA12878_diploid_genome_may3_2011. They are all single base pair mismatches between the paternal and maternal chromosomes in regions that the accompanying .map file marks as contigs.
.map file shows continuous equivalent (without gaps) blocks between haplotypes. BUT THEY DO INCLUDE SNPs. So, heterozygous SNPs will result in base mismatch within a block.