Are we even sure at this point that the stone did anything more then react to her being "The Scarlet Witch" ? Apparently, now even in the comics that's some sort of magic title.* Wanda and Pietro's ability to absorb power from the mind stone without perishing does make more sense knowing that they already had some level of powers beforehand.
This is exactly what I was thinking. I think what happened is they retconned it so Hydra never actually gave them their powers, as the Mind Stone kept killing all the other volunteers. Wanda had some sort of latent magic, being born as the Scarlet Witch, that gives her powers over probability, reality, and creation. When she came into contact with the Mind Stone, the being that showed itself inside the stone unlocked her powers, using the Mind Stone more as a conduit, and Hydra just worked off whatever fluke happened with her and the stone.And i found it interesting that they (as in Hydra) don't mention trying it on the brother after. Seeing how she can just manifest a whole new Vision, there's no reason to assume she didn't just give Pietro his speed herself.