John Hawks, along with Gene Expression regular Greg Cochran, has published a paper (PDF) on adaptive introgression in human evolution. In case the jargon is too much, we're talking about the caveman gene. Both Greg and John have blogged the paper. Check out what John says about mtDNA:
However, there have been a growing number of examples of adaptive introgression between different natural populations as well. The use of more nuclear markers has begun to uncover many, but importantly many species have adaptive introgression of mitochondrial DNA.
[emphasis from original]
Adaptive introgression of mtDNA sure would screw up any demographic inferences one makes using mtDNA polymorphism. Adaptive introgression of any single marker would screw up demographic inferences. Yes, it's another reason for people to stop using mtDNA, and mtDNA alone, to study population history.