An app is an integrated DeFi application on Zapper. The app will show assets that you have deposited into the app's respective protocol.
A token is the asset you are depositing into the protocol using the app. Each supported DeFi app and their products will have a breakdown of how the assets are invested on the app page.
A general rule-of-thumb is if an app has positions in it that are not liquid and tradable on exchanges like, pool tokens or vaults, those will only show up on Zapper through an app integration via Zapper Studio. Alternatively, almost all tokens that are freely traded on exchanges automatically populate onto Zapper.