Why does my Sapphire Crystal disappear when I purchase Catalyst the Protector?

Sapphire Crystal is one of the ingredients for Catalyst. You can purchase the full recipe at any time, and it will automatically subtract the cost of materials you already own from the purchase price of the recipes and use those rather than new materials.

This is due to the way that items build together in League of Legends. More powerful items are built by obtaining the "ingredients" needed for them (in the case of Catalyst the Protector, the ingredients are a Sapphire Crystal and a Ruby Crystal) and a "recipe" cost (in this case, the recipe cost for Catalyst is 450g). When the more powerful item is purchased, the ingredients are "combined together" to make the new item, so they no longer appear in your inventory.