Corrupted Nexus fails to complete

The first time I've done a Corrupted Nexus map (quest to do tier 3+ waystone) with a boss inherent in it (Decay), I've killed all the rare monsters before doing the boss, the Nexus boss didn't spawn.

Then I've killed the boss, but maybe because I died once and had to respawn the boss fight it still doesn't count as complete and no Nexus boss spawned.

However the atlas treats it as complete and the area around has the cleansed graphics.