When Amy was kidnapped and her ganger used to travel in TARDIS, The Doctor often used to scan her for her pregnancy. The result: Positive - Negative both/alternating.
I don't know they wanted to show scanner malfunction on alien domain or quantum superposition of both positive, negative pregnancy, but in either case why would that be the case?
In the episode, in which The Doctor found out that Amy was a ganger, we saw the Flesh was able to copy anything which included a Gallifreyan with Time Lord upgrade. The copy was perfect. The new The/A Doctor was even equally smart. And, we saw this from primitive Earth tech, not a time traveling faction (Amy's version should be better).
While copying pregnant Amy, why wasn't it perfect?
Why the hell both pregnant and non-pregnant state? Either the tech could copy the embryo (or whatever state) or simply couldn't. What exactly did it copy?