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...
Ok apparently I've had a history of misperceiving Water/Rock types.
First of all, I've had SO much trouble determining where the hell Kabuto's eyes are. Are they the measly dots on top of its shell, or the bright red eyes searching directly into my soul? I still cannot accept the truth(especially after seeing Kabutops' eyes).
Different Pokemon, same predicament. I thought that Relicanth was secretely plotting my death with those staring red eyes... Isn't wasn't until I saw his back sprite that he changed from a creepy demon to a grandfather-faced fish.
...Pathetic. His eyes look just like Brock's.
Finally, there's Corsola's Gold sprite. Being the first time I saw Corsola, I thought it was just a pink ball with spikes coming out. I didn't notice ANY moveable arms and legs on it until later sprites came out.
According to Bulbapedia they're BOTH pairs real eyes apparently, which I suppose isn't too crazy given arthropods are prone to that sort of thing in real life. The black ones are for when it's buried in sand at the bottom of the ocean or something, and the red ones are for... scaring the living daylights out of little kids I suppose?
Speaking of, I thought for quite some time that Seviper was Arbok's evo...until I bred two of them, and out comes...another Seviper. Like, wait, it's a standalone? Took me a while (and some trolling on Serebii) to realize my derpiness.