This error has been tracked down, thanks to the alpha testers, and should be fixed in next build. It was caused by multiple races targeting the same planet while out of range of the planet.
I'm sorry but, this isn't the cause... In my current game I started with only 1 AI player, the AI player never had more than the initial colony ship. AI colonized the planet in the system, I took the home planet via transport w/ in 5 turns. They have since never launched another colony ship. Two planets in a completely different system will not allow colonization.
In order for that to be the only reason this is occurring it would mean that the AI player targeted both planets prior to colonizing the planet in it's system or has phantom colony ships ready to colonize said planets...
Just thought I'd share this bit of information.