My attempt at guessing the next episode (Amy's story) by adding on various theories and speculation:
Amy is a clone. We don't know when she's been cloned. Silents cloned her. She has a
psychic link to the real Amy hence all these Kovarian appearances. The Doctor knows this. The scanner is scanning both the clone Amy and through the psychic link, the real Amy. One is pregnant, the other is not.
Amy told the Doctor she was pregnant because the psychic link leading to the real Amy is actually pregnant. At the end of episode 6, we see the clone Amy die or something, and the viewers find out she was a clone. That the real Amy has been ...
The most important observation to back this is the Doctor's hints. He knew about the Flesh technology. At least, a later version of the technology. He wanted to investigate it without Amy and Rory. He was questioned about knowing about a later version of the technology in the bathroom by the man and Amy. He gave Amy a long stare.
To back up the psychic link between Amy and Clone Amy, he tells clone Amy in Rebel Flesh to '
breathe'. The same sort of messages that Kovarian has been giving the real Amy as if to guide her through pregnancy. "I think she's just dreaming/It's fine. You're doing fine. Just stay calm".
Why tell her to breathe? I think he was giving the clone a message which would no doubt be passed onto the real Amy. Just like the Kovarian messages are passed from real Amy to Clone Amy.
Finally a spoiler from a trailer
Will come back to this post on Saturday to
or to