Amy runs up to the Doctor and tells him she's not pregnant, out of the blue, because of all the cliffhangers last week apparently this is the only one that actually matters or needs to be discussed, because the only interesting thing about her is what we can fit inside her, whether it be the universe or Rory's giant-nosed progeny.
"Sometimes you feel a bit sick, though, but not always," Amy "clarifies" -- stop with the hard-science declarative facts! -- in response to a question nobody asked regarding the perceptual effects, but coming so close to the pregnancy thing is either a red herring about the pregnancy, a mistake, or an actual nod to the possibility that her cramps had nothing to do with the Silence. Which brings in the question of whether the also-cramping River Song is also pregnant, which I would love to say seems unlikely but on this show, given that she's a woman, is not that unlikely.
This also explains, apparently, the hash marks all over their arms and faces: When you can't remember to look out for something, what might help is mysterious shit appearing all over you that only makes sense when you're remembering what's actually happening in front of you. Unless, like in some scenes of this episode but not others, you're one of those characters who keeps forgetting over and over, like Bathroom Lady, versus the TARDIS team, who remember there's something to remember but only sometimes what that thing is. Or Canton, who falls somewhere between the two groups except when it moves the plot along for him to be one or the other.
None of which really makes any sense, of course, but second of all: Why on the face? In what circumstance would you make marks on your face, and also how would that help you remember anything or keep it straight? There are two places in the universe you just absolutely cannot see, unaided, with your own eyes: Your face and the back of your head.
The answer, of course, is that if you start with "hash marks all over Amy's face" as a plot point and then retrofit it into whatever episode you feel like, which is how this show is written now, it doesn't matter. (And also, because weird stuff magically appearing on your face has already happened like five times in the past four years on this show, so why not.)
Everybody's spent the last three months trying to figure out what is going on here, but as the characters themselves remark, that's difficult when you can't remember what you're doing or why you're there. Instead of following this through to its logical or satisfying conclusion, the answer is again that you can't remember, unless it's sometimes, and then you kind of can, depending. To distract from that mess, let's have a big speech.