Population Bug and minor annoyance

Ok so I conquered a species that had a different atmospheric tolerance than my main species and planned on using them to colonize some mineral rich worlds in another system (I had colonies in 4 systems). I colonized those planets and everything was fine until they started migrating. They went from one system to another and began to settle in my colonies that had oxygen atmospheres (none went to my home system though). This made 4 of my colonies suddenly dome planets significantly reducing their production. Is there a way to prevent migration between systems or do I need to ethnically cleanse my empire?

Now for the bug. I was playing as the terrans and I conquered the xaite (spelling?) which have the same planet prefrences as the terrans. After the incident above I figured why not let a species that can't possibly cause my colonies to "dome" live? I moved the entire xaite pop out of their home system and onto a new huge oxygen rock planet with a small terran population. All was well until the xaite's loyalty and happiness began to plumet about 3 turns after being put onto the planet. They wouldnt do anything so I just decided to grant them independence to the other aliens with the green flag thing (you can tell I'm great with names). Before I granted independence I evacuated the 55 million terrans living on the planet. In the next 2 turns the planet went independent but... it was a new independent empire and the 4000 xaite vanished and instead were replaced by 8000 TERRANS with loyalty to the new empire??? The only thing in my log was a message stating that I had contact with a new empire. The xaite were no where to be seen on any of my other colonies. There was also no evidence of a mass terran migration from my other colonies. Is this a bug or a random event? Or is this supposed to happen when granting independence?