It seems that every so often when I glance down at my pheromone groups that there's a phantom brood chamber of the same kind of ant without any members that's below the one that's actually there. Moving the real brood to a different group and back again tends to fix the problem, but it's still a bug. I also haven't seen it happen in the Formicarium so far, only the levels, and I've only played the first two levels since the update.