Atlas progression stuck

I only have 4 atlas passives. I think my atlas prog might be bugged. I've cleared two corrupted nexus so far and haven't gotten any credit. The last one I did was t14 +6 mod without dying. Cleared the entire map and double backed and didn't see anything.

Anyone else experience this?

Checkout your quest progression, its base on the quest
I reach lv 89 with only 15 atlas point as well, hahah