The message you receive shouldn’t be stopping you from entering a payment, at least not on the web version or in iOS (sorry, I don’t have any experience with Android so I can’t test the behavior there).
Ordinarily Goodbudget will calculate the percentage of payment that goes into each category, so what you’ll need to do here is manually enter your entire additional payment as Principal, and enter 0.00 in both the Interest and Fees block. That should allow you to post the additional payment as you expect.
Hope that helps!