According to an old report, AP items obtained from Archaeology aren't always detected properly. More specifically, this was the example given: Crystalline Demonic Eye @ wowhead.com

The issue is clearly that those items don't use the typical "Empowering" spell, nor do they use the "Artifact Power" tag in the item description. Therefore, they aren't detected by the extraction scripts currently and would have to be manually added... which I haven't done, as Archaeology takes way too much time unfortunately.

If all the items can be easily found via wowhead, they could be added manually, although I'd prefer to find a way of grabbing them automatically.