I have the exact same problem and this has been going on since day 1. I have 4-5 available slots to fill and yet I can't consume anything.
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Xerfer, To my dismay, I finally (after 4 months) figured out my problem. I was pressing A instead of X to use my consumables. You can imagine what an ass I felt like after figuring that one out. Just incase your doing the same thing (because A is an action/equip button and I naturally was using that without paying attention)