Since they are starting up right where they left off at the end of season 13, I can't see how Amelia could possibly be pregnant considering she hasn't been at home in like 5 or 6 months. Unless there's a time jump between 14x02 and 14x03, but even that seems like a bit of a stretch.
I think (based on promo pics for 14x03) that Megan has a brain tumor and she can't tell Owen and Riggs for some reason.