Amy's always been an expressive creature, she feels so much and all of it plays out on her expression so when Rip says he had a son, past tense, her heart twists in her chest and she's struck with a miasma of simultaneous emotions. Sympathetic grief for a man who lost his son, selfish grief thinking about the feel of Melody dissolving in her arms, gratitude that eventually she got her daughter back even if she was a grown woman.

And guilt that she feels grateful she at least had that and didn't lose Melody completely.

"I'm sorry." It's not a pitying condolence, full of some kind of quiet empathy and compassion that speaks to the experience that still isn't quite the same. "River is my and Rory's daughter."

Their daughter who is old enough to have a future husband and opinions on alternate realities she brought into existence even though Amy is not nearly old enough to have a daughter capable of any of that. Maybe a ten year old, she's old enough to have a ten year old seeing as she and Rory just had their ten year anniversary.