You need to upgrade Fairy Portal to increase your storage capacity so you can collect more Ambrosia and Night Essence. The portal has a limit on how many guest race goods you can store. When you click on the portal, you can see the limits. Or you can use some of the Ambrosia and Night Essence to free up space so you can collect more production.
You can visit elevengems.com for extensive guides on every guest race chapter. The guides show you the size of your buildings that are eligible for upgrade that chapter so you can plan your city accordingly.