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There are a couple reasons why Hamsters (and most similar rodents) will kill and/or devour their young.
One reason is rejection of scent, which can be attributed to humans handling the young too much before they've been able to develop their own recognizable scent.
Another is because the particular young has become sick, is weaker than the others, or has gotten injured (especially if the injury broke the skin). The mother may 'dispose' of her young if they present some kind of threat to her and, in this case, if she thinks the scent of the injured or sick baby will draw predators.