Completed Tier 2+ Corrupted Nexus didn't get Atlas points

I used a tier 2 stone with 4 modifiers, completed the map without dying, there was a boss at the end, killed the boss and it didn't drop the atlas points.

Now I made sure this was a corrupted nexus, bright red corruption icon, and once I cleared the map all the corruption in the are was gone.

You need a tier 3 waystone, because it needs tier 2+, so tier 2 doesn't clear it

This happened to me twice. I need a 5+ nexus and completed a t14 map with a boss modifier on the nexus. Instead of spawning the nexus boss, only the corresponding map boss appeared and the map was cleared after defeating the boss. I did not get the atlas passive item and the corruption was still cleansed. This makes it very hard to progress in the quest.

I probably need to find a nexus without a boss modifier...