Hi, Amber!
Yep, that whole situation was very confusing and I don't think the writers sufficiently explained it.
I have my own theory why Robin said "No" and it involved her wanted Ted to give up on her after she realized she couldn't have children, but if the writers were going to have that scene happen, they really needed to explain it so that Ted and Robin reuniting in the future wouldn't be so confusing to people who didn't like the ending.