I don't think I have enough information to comment, but this may be a server syncing issue. If you expanded your sewage capacity in one city, and this is not being recognized in the other city, this is because the game recognizes an older version the said city.
Server syncing is known to cause other similar issues when resources are shared with cities, such as workers not commuting, gifts disappearing, etc. As far as I'm concerned, there is no fix for this. I had such a problem when one of my cities didn't recognize that a region department was placed in another.
