hi and welcome.
currently cities can be joined only when a member of the waze team does it on the back-end. There's no automated process.
As you might know, we are still having problems with the display of provinces, states, counties etc... which is why two cities with the same name are not allowed on our maps.
For this reason, we currently recommend people to name their city 'Alphaville, county A' and 'Alphaville, county B'. Once we have full support for the counties, in the DB and in the cartouche, you will be able to better city the full tree (sometime there's a neighborhood in a city in a province in a county... and so forth).
As for your city, it's possible that someone asked me to merge them and I did. If this was a mistake, I apologize, but I cannot reverse it. If you do create a new city, make sure to add some kind of identifier after the city name, to differentiate it from the other cities with the same name in your country.