If you look at the end of FFVII you can see part of Midgar being rebuilt during the 500 years clip.Actually no its not. Midgar cannot be three different cities in the future because it was destoyed at the end of 7 and never rebuilt.
And it's entirly possible for a city to be devided. concidering what happens at the end of FFVII A lot of place get sepperated. And If you look you can see obvious evidense these places WERE Midgar at one point (Deling and FH is obvious)