With the newest changes to colonies, your empire can only have one colony on any given world. However, the game is smart enough to keep civilian mining installations separate from your mining operations - you'll either mine with both your own mines and the civs (if you're buying the minerals) or the civ's minerals will be sold, but your own mines will produce (if you're selling them).
The civilians like naming colonies after themselves, instead of after the system body that it's stationed on. You can rename the site back to the body, if you find it confusing.
