Yeah, its a thing they do from time to time. When you first arrived at the Crystarium if you had walked away from the Crystal Exarch and immediately tried to attune to THAT aetheryte it would have not allowed you as well. But that one unlocks by finishing a single quest, so most people dont even have time to realize that its locked before they unlock it. Youll encounter it a few more times when they think its appropriate for the story.