There are instructions on this page for managing and stopping auto-renewing subscriptions : http://support.apple.com/kb/HT4098
You don't pay for downloading updates to apps (e.g. updates downloaded via the Updates tab in the App Store app). If you are using in-app purchases within the apps to unlock extra features or to turn them into 'full' apps then you will pay for those.
You can check the purchase history on your account via the Store > View Account menu option on your computer's iTunes though I'm not sure if that shows auto-renewing subscriptions (I don't have any so I can't check). If you are adding or changing your credit card details on your account then a small temporary store holding charge may be applied to check that the card details are correct and valid, but they should disappear within a few days or so. If you think that you are being charged when you shouldn't be then you can contact iTunes Support via this page : http://www.apple.com/support/itunes/contact/ - click on Contact iTunes Store Support on the right-hand side of the page, then Purchases, Billing & Redemption