1) The advisors section marks checkpoints from left to right as you complete them. The boxes do not correspond to the checkpoints in order, If you do the raid out of order. 2) Each character can complete a raid and earn loot, one per character per difficulty per week. Doing hard mode first, however, earns you the loot for both normal and hard at the same time. Therefore, what you are seeing is correct - you did hard mode first, and were awarded both normal and hard drops for that checkpoint, and the advisors tab is marking it as such.