You don't receive Atlas skill points if there's still a rare remaining after killing the boss

Title basically. I had 4 Atlas skill points and ran a T16 map yesterday on a corrupted node, but the boss didn't drop a skill point book (it didn't drop any maps, either). However, there was 1 rare remaining so killing the boss didn't count as completing the map.

I just ran another T16 + corrupted node and killed the boss without any remaining rares and I received the skill points.