I have already used all the stones everywhere which infuriates me for being so stupid for some of the items I saved, and seeing that charts I have encountered every item on it except for the Sphere's, Old Amber, and Skull Fossil.
I have also encountered those fossils multiple times Dome, Helix, Claw, Root, & Armor, I have encountered them at least five times each.
Edit: You know I just remembered that in 4th Gen the fossil was determined by your Trainer ID so I wonder if Amethyst did something like that, cause I find Armor fossils too easily.