Corrupted nexus not awarding atlas points

Failed a t6 nexus ran out of revives, was able to load into and play the nexus afterwards using a white waystone with zero mods, completed the nexus, nexus cleared like a normal map, the surrounding zone is still corrupted. Pretty sure that's not right.
Went to a new nexus t6 4 mods, died for the first and only time while fighting the boss. Completed the nexus less than a minute later, all the surrounding maps are now cleansed, still no atlas points. Whatever you've done you have really broken the atlas, it is actually unplayable.