Interesting, and at first blush, a contradiction: First, the historical mainstream view, unsubstantiated by the kind of scientific and physical evidence that archaeology or genetic analysis brings to the discussion, used to be that Gujjars and Rajputs are both, separately, descendants of the Scythian-Pahlavi tribes who were driven to Sakasthan (latter day, and present Seistan) and conquered and ruled most of western India for a period. They were later subjugated by the Kushans (who had driven them from their homelands in the first place) but ruled as more or less independent rulers paying tribute to the central imperial authority.
Second, there must inevitably have been considerable intermarriage with the local inhabitants at the time of their incursion. That could lead to different lineages among people of the same endogamous group.
This could explain both the reputed origin as well as the contradictory DNA. Incidentally, if more and more individuals get themselves tested, and it appears that the majority are descended from local inhabitants and had nothing to do with the Saka-Pahlava, the historians will be forced to revise their thinking and re-write their books.
