Both Amaranthus palmeri and A. watsonii are nested within the complex, so when there is a disagreement between the two, the complex, being the lowest common taxon, is the CID.
Please note, “Complex Amaranthus hybridus” is not the same thing as Amaranthus hybridus, the species. For more info, see this post: https://forum.inaturalist.org/t/why-is-the-word-complex-added-to-some-binomial-names/55702/5.
This is not a bug. I am not at all familiar with the taxonomy of this group, but if you believe the species truly should not lie within this complex, you should flag the taxon and discuss there, as you have already done.