You pull out the blue potion bottle and uncork it. Right as you are about to pour, you unlock a new POTION stat which shows how much of the potion you have remaining! Because the amount of potion in your possession is now determined by your POTION stat, the blue potion bottle stops being classified as an "item" within your inventory, freeing up the inventory space for other non-potion items.

This all feels a bit abstract and confusing to you, but if the end result is that you can hold more stuff, you're not complaining.