It just came to me on my rewatch. If the flesh is so intelligent that it even replicates a clot on the brain of whatshername, then why didn't it replicate Amy's pregnancy? She even had the contractions, but no baby or bump
I thought about that when I was watching The Rebel Flesh again just now. The only solutions I could come up were 1. that the flesh can't carry children (makes little sense though as they are meant to be complete copies - Amy's is a future version though so maybe they've been modified somehow) or 2. it did copy the baby but they removed it - maybe to keep the Doctor off their scent for as long as possible. They must have known the contractions would pass through to the copy though.
Probably reaching here, but it was the best I could do