It looks like Factorio 2.0 changed how the recipes look by default.
Changing your recipe to this seems to let it run with quality loaded.
{
type = "recipe",
name = "stone-waterwell",
energy_required = 10,
ingredients =
{
{type = "item", name = "iron-stick", amount = 4},
{type = "item", name = "stone-brick", amount = 8},
{type = "item", name = "stone", amount = 40},
{type = "item", name = "offshore-pump", amount = 1}
},
results = {{type="item", name="stone-waterwell", amount=1}}
},