In my latest game as the glorious Altarians (I love their late game science) I've encountered what presumably is a bug.
I have surrendering colonies turned on and am at version 4.1.
At one point two civs I was at war with both surrendered. The Korath gave all their assets to the Iconians and then immediately afterwards the Measured gave all their assets to the Korath! The outcome was that as a principled benevolent bod i didn't want to got to war with the Iconians but the previously Measured planets become Korath as they rose from the ashes and I was able to continue merrily taking those without upsetting the Iconians.
This is a link to the save just beforehand. If you move a couple of ships and then enter it should replicated this behaviour