That's a question for Customer Service or Mike Stangel. I think the answer is that they're only propagating back for so many generations,
This was my question to them:
"How many generations is geni extrapolating mtDNA over?
If the mutation rate is as big as every 10 000 yrs or - on genealogical trees - as small as every 25 to 40 generations (about 500 to 800 yrs), that's still way more than the only 10? generations geni seems to propagating it up the tree.
I ask because the geni propagated mtDNA is falling just short of a number of the South African Progenitor profiles whose mtDNA haplogroups we have been trying to collect for some years now: https://www.geni.com/projects/South-African-mtDNA-Female-Progenitor...
The oldest of these women is likely to be born in about 1640: Krotoa 'Eva' van Meerhof SM/PROG - which is definitely under the most conservative estimate of 500 years."