This has been happening for quite a while. I'm not sure which update caused it. I've seen it in two games so far. When you go to war with a civilization and beat the heck out of them, they usually surrender to you or to another civilization friendly to them. Alas, all those surrendered planets fall into a black hole and disappear. They are no longer on the map. So if you had a hankering for that class 26 planet now in your zone of control, there is no way to get it, even if it has been surrendered to you.

This is a major bug that should be fixed, because it ruins your strategy of occupying every planet on the map. I'm currently playing the Milky Way campaign and it happened around about turn 378 or so when the Altarians turned their planets over to the Iconians.