Versions

Betweenlands version:

TheBetweenlands-3.5.4

Forge version:

1.12.2
forge-14.23.5.2847

Singleplayer or Multiplayer:

Singleplayer

Installed mods:

Betweenlands, Akashic Tome, Appleskin, Astral Sorcery, AutoRegLib, Baubles, Better Advancements, Better FPS, Bountiful Baubles, Chocolate Quest Repoured, CodeChicken Lib, ConnectedTexturesMod, Dimensional Doors, Dynamic Surroundings, Ender Storage, Fast Leaf Decay, Fossils and Archeology Revival, Gravestone Mod, Iron Chests, Iron Backpacks, JEI Villagers, Journey Map, Just Enough Resources, Librarian Lib, LLibrary, Mantle, Millénaire, More Creeps and Weirdos Revival, Mouse Tweaks, Nature's Compass, Neat, OreLib, Patchouli, Serene Seasons, Shadowfact's Forgelin, The One Probe, The Twilight Forest, Trinkets and Baubles, Villager Market, Waystones.

Description of the problem

Ingredients show as used in the herblore book when there's still aspects to be found.
That one might not exactly be a bug, but it's a bit of a design flaw. They should only be cleared out when you actually cleared them out.