I never had the misconception for Anorith, its eyes always seemed blindingly obvious to me. The eyes on ARMALDO however, are much less obvious, especially in its sprites. It's also a lot less common in the games so you would not have seen it as much. It doesn't help that Armaldo has those 3 sets of fins or feathers or w/e those thing are on its neck, making it not unreasonable to assume its eyes are just another pair of those things unless you look closely.
Now that I DO know about it it's pretty obvious, and especially face-palm worthy for me since I had ALWAYS known that the red dots on Anorith aren't its eyes (so it wouldn't make sense for them to be eyes on Armaldo). I guess I just never really thought about or questioned it.
Honestly I kind of wish that those red dots HAD become its eyes though because it looks a LOT less derpy that way...