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The real Amy was pregnant from her wedding night, shortly after the close of "The Big Bang", to just after the end of "The Almost People", when we saw her going into labour.

The ganger of Amy -- the Amy we saw from "The Impossible Astronaut" to "The Almost People" -- was not pregnant. That ganger was, however, connected with the real Amy, which is why the TARDIS couldn't decide whether or not she was pregnant when the ganger was scanned.