Yes, this is an apparent discrepancy of CVTree from 16S (and 23S) analysis for the given set of 179 archaeal genomes. However, in an on-going study of ours (not published yet) using a much larger data set this violation no longer shows up; both Korarchaeota and Crenarchaeota restore their phylum status. Taking into account the fact that both Korarchaeota and Thermofilaceae are represented by single species for the time being, their placement certainly requires further study with broader sampling of genomes.
Results also provide additional support to recently proposed archaeal phyla and halobacterial orders.