Happens in 0.5.4 version but might also happen for 0.6.0 (I just can't check because it doesn't even load with Pyanodons enabled):
When selecting building with permutated recipe with copy tool, the game shows big cross mark over the recipe when trying to paste the building. This is because players don't have access to the recipe (can't select it in the building itself) so game thinks you cheated (or used editor) to set the recipe.