This is a very good point. I'll attempt to make up an explanation, haha:
-in an earlier episode, Ethan tells Kate that it's been weeks, not 12 years, since she's been missing (at least I think he did, if he didn't then this explanation is screwed)
-Kate believes she's in some kind of experiment
-she could rationalize that part of this experiment is somehow having an Ethan, Theresa, and Ben that haven't aged 12 years since their story is it's only been weeks
-after all, if Ethan bursts into town saying it's only been weeks, but he and his family look 12 years older, how is his weeks story believable?
-how does she rationalize the experiment achieve this? well, it's sci-fi, so there's lots of possible explanations:
-eg. perhaps Kate's thinking the 12 years are now maybe some kind of false memory
-eg. in flashbacks, she did ask if the experiment was social or medical, and this could have a top-secret medical explanation
-eg. perhaps these are the best body doubles/actors she's ever met
-eg. simply leave it as a mcguffin