They could handwave the fact that none of the other versions remembered him. It would be a relatively straightforward way to get Clara into those other versions. Roonas and I talked before about the idea that she might be exposed to the time vortex somehow like Rose was, but with a different result. It could be anything, though. I'm sure the show has no end of things it could make up that could spit copies of her out in all different places. She might even do it as a conscious choice, because she can suspect now that he's met her, or someone like her, in different times.

That leaves open the question of who gave her the TARDIS's number so she could contact the Doctor in the first place. River and Rose being the two most likely suspects.