Phylogenies of the Neandertal haplotypes

If you look at the phylogenies of the Neandertal haplotypes discussed in the Zeberg and Pääbo studies, they look a bit different. For the haplotype on chromosome 3, it is clear that they came from a particular population of Neandertals (perhaps a population related to the individual sequenced from the Vindija cave). The phylogenetic tree looks a bit different for the haplotype on chromosome 12. In fact, haplotype XXIX and XXX are sort of in their own group. Why is this?