According to the BBC, Gangers is about when people create doppelgangers for dangerous work, but when something happens to the original, the 'ganger gets their memories - so are they really the person, or just a malfunctioning tool. I think what we're seeing with Kovarian is a hint that we're not sure whether these are Amy's memories, or her ganger's memories of the original her... Which means the reason the TARDIS doesn't know whether she's up the duff is because presumably one Amy is or was, and the other isn't or wasn't, but remembers being so...