Because Judo judges like to stand people up if there's not progress being made instantly and someone is obviously going for a pin. It's high school Judo in Japan, not adults doing BJJ in the US. You only ne-waza when there is no score, but the ref called waza-ari for a half point. The idea is an ippon is something that would likely end a fight if done with bad intent on a hard surface, and thus ends the match, and a waza-ari is something that might not end a fight, but would be a big deal so they are just stood back up. I personally might not have called that waza-ari and let them wrestle a bit myself, but I'm also not a Japanese youth Judo ref.
And her stance was way too low and forward for Nagatoro to sweep that leg, all her weight is on that front leg so it's not getting swept, especially with her center of gravity so low. She was exactly where you don't want to be to Kouchi Gari someone, you want their feet closer together and no more than 60% of their weight. Ideally you catch it when their weight is off it to break their base and push them down that way.