Through the creation of fortresses/cities your alliance loses some habitats as they are merged into a single, big habitat. New free habitats are created in the process. If your alliance is fast enough, you can capture them directly and further enhance your power!

An example:
A region consists of 100 habitats. Your alliance controls 80% of the region, thus 80 habitats. If 5 castles are now merged into a fortress, your alliance will only own 76 habitats and thus 76% of the region. You would therefore lose the region within the next 2 Region Updates, unless you recapture the newly created free habitats.

If your alliance controls 85 out of 100 habitats and then creates a fortress, it would still have 81 habitats (81%) afterwards. In this case you would not lose the region.