I was charged on two different credit cards for the same app purchase but only purchase on one apple account

Do you have more than one payment method set up for your Apple ID account? Have you reviewed your purchase history? Here is a one-stop link for billing questions→Subscriptions and Billing - Official Apple Support. You can review your purchase history to see what you were charged for, cancel subscriptions and request refunds.

Do you use multiple Apple ID?

You can have a credit card / debit card on file and an Apple Account balance.

Your default payment method will be used first by Apple when you need to make a payment.  

If you have set your Apple Account balance as your default payment method and you have a CC / debit card, you pay from your default payment method.

If you have 2 CC, and you have set one CC as your default payment method that will be charge by Apple.

Get support from Apple directly -> Get Support or call Apple in your region see -> Contact Apple for support and service or check -> here for more support and assistance.