Even more likely is that you have a level zero portal and can't store any ambrosia at all. I think just about every player gets caught by that the first time they enter fairies. I'm pretty sure if you are on browser, there is no an option when you click the building to discard production (losing all the inputs). Otherwise it is stuck until you upgrade the portal. If you are desperate, and have some teleport spells, you could try teleporting the factory and building a new one to replace it.