Hi, it's probably weapon evolutions or rare pickups.
If you're missing a slot next to one of these weapons: Magic Wand, Knife, Axe, King Bible, or Fire Wand
Then you're missing the evolution of that weapon.
If you're mising a slot near the bottom of the collection, then you're missing a rare pickup and increasing your Luck and trying to destroy as many braziers as possible should help.
How to evolve weapons
Level up a weapon until it's maxed out and satisfy its requirements for evolution, that are different for each weapon. Once all requirements are satisfied, there will be a chance to find the evolved version of the weapon in Treasure Chests. For example:
Magic Wand LV8 + Empty Tome + Treasure Chest = Holy Wand