Amy can't have kids because of what they did to her at Demon's Run. It was very vague, but it was implied during Asylum of the Daleks (season 7, Epi 1) when Amy and Rory are fighting about their divorce and she talks about not being able to have kids "because of what they did to me at Demon's Run".
Yeah, the River thing was strange but I guess when you're a time traveller being older than your parents is bound to happen now and then! I love River and Eleven together, she is such a badass.
Does anyone else have trouble with Clara? She is a really underdeveloped companion to me!!