Yeah, there’s a lot of talk about this around the forum if you want to read up on it - some good search terms are nested & duplicate street … these are probably the best places to start: Discussing 'nested' cities and Fixing street double count
It sounds like either one city isn’t entirely nested in the other, or it was just missed for some reason.
It would be easiest for me if you can share the links to those two cities. I can look into whether I can mark one as nested.