This description was correct in the first place! Turns out it was the upgrading recipes' fault.

src/main/java/electroblob/wizardry/integration/jei/ArcaneWorkbenchRecipeCategory.java

@@ -198,8 +198,10 @@ public class ArcaneWorkbenchRecipeCategory implements IRecipeCategory<ArcaneWork
 					}
 				}
 
-				recipes.add(new ArcaneWorkbenchRecipe(original, Collections.emptyList(), Collections.emptyList(),
+				if(!applicableSpecialUpgrades.isEmpty()){
-						applicableSpecialUpgrades, original)); // Wands with special upgrades look no different anyway
+					recipes.add(new ArcaneWorkbenchRecipe(original, Collections.emptyList(), Collections.emptyList(),
+							applicableSpecialUpgrades, original)); // Wands with special upgrades look no different anyway
+				}
 
 			}
 		}
@@ -253,8 +255,6 @@ public class ArcaneWorkbenchRecipeCategory implements IRecipeCategory<ArcaneWork
 
 		for(Spell spell : Spell.getAllSpells()){
 
-			if(spell == Spells.none) continue;
-
 			for(Item spellBook : spellBooks){
 				for(Item scroll : scrolls){
 					if(spell.applicableForItem(spellBook) && spell.applicableForItem(scroll)){

src/main/java/electroblob/wizardry/spell/Spell.java

@@ -1007,7 +1007,7 @@ public abstract class Spell extends IForgeRegistryEntry.Impl<Spell> implements C
 		return registry.getValuesCollection().stream().filter(filter.and(s -> s != Spells.none)).collect(Collectors.toList());
 	}
 
-	/** Returns all registered spells, including the {@link None} spell. */
+	/** Returns all registered spells, excluding the {@link None} spell. */
 	public static List<Spell> getAllSpells(){
 		return getSpells(s -> true);
 	}