If you are a South Asian waiting for your results from Genographic project then you can find your ancestor hunting down Neandertals in European lands instead of Heidelbergens in India. It seems over subscription by Europeans is the reason behind non-testing of South Asian specific Haplogroups unless they are found predominantly in India.
So if you are any of R1a1, L* and H* then it's highly likely that your ancestor's journey ends in the sub-continent. May be it's true for Indian females with mtDNA Haplogroup M*. However, if you belong to Y-Haplogroup R2 or mtDNA Haplogroup U7, then there are all the possibilities that your markers won't be tested and you would be assigned some upstream Haplogroup would be sent somewhere. Couple of examples from FTDNA forum,
For Y-Haplogroup R2,
For mtDNA-Haplogroup U7,
However, the funniest thing would be assigning Haplogroup R1* for R2. I know it's not as bad as blundering the paternal testing, but it doesn't make much sense. Does it?