I use the Kobo app not the border one because thats the one that came with my Kobo. I've bought only few books but I've never that problem, except I did purchase one by accident trying to see what the price would be after I subtracted a coupon code, but it was minor, only 3 bucks. If this keeps happening you could probably just download the
Kobo app instead of the borders one, I don't think it makes much of a difference other than the color. And you will still be able to pay in your country's currency.
Did you update it the app to 1.9 the newest update, or is it still 1.8? The new app is having a few problems right now, you can see what version you are using by clicking the "I" for info in the top right corner of you library. If its 1.9 you'll just have to make the best of it for a few days until they fix the app.
Hope this helped