You have nothing to worry about, She's just rearranging them. Most animals carry their young by the scruff of their neck to move them from place to place. There's no need to separate them as she's just doing what any mother hamster would. The part that she's using to carry them is typically referred to as the 'scruff' and doesn't hurt the pup in any way, though they might squeak a bit. Cats and dogs also carry their young this way.
