I am pretty certain that can't happen with chins. There is a condition called superfoetation that MAY explain it...
Chinchillas have two uterine horns, which each hold viable eggs. Sometimes one horn's efggs can become fertilized and begin developing into kits, while the other horn's eggs remain unfertilized. Then, at a later date, the female can mate again and the other horn's eggs become fertilized as well. This results in two kits at in the same womb, but at two different stages of development. My understanding, however, is that when the female delivers the more developed kit, she would also deliver the lesser one, resulting in either drastically different sizes, because one kit is essentially premature, or more likley the lesser developed one is stillborn. I don't think she can deliver one and retain the other for continued development.
In all likelihood, the tricky girl just managed to seduce one of your males when you had your head turned. If you have never seen a chin mating, they don't take long at all, a few seconds. And as someone said in an earlier post, where there's a will, there's a way.
