And yet it's stated in AGMGTW that the first time she and Rory stepped aboard the TARDIS in the current Universe was on their wedding night, meaning that while they remember the events of Series 5 they didn't physically happen to them.
Yet "A Good Man Goes to War" also
tells us that the incident with the Atraxi from "The Eleventh Hour" happened since the Thin/Fat Gay Married Anglican Marines talk about the Doctor calling them back to Earth and scolding them. To be fair, though, Amy and Rory don't set foot in the TARDIS in "The Eleventh Hour" so that's not exactly a discontinuity.
Now I understand why time travel gives Geordi La Forge nosebleeds.