Do you have a debit or credit card linked to Android Pay? Did you check to see on that actual institution website to see the extra $.25 extra charged to you? I haven't received any overcharge at all. The amount that the item cost is what I have paid. So far I have only used Android Pay at vending machines but still haven't seen any over charge.
I know that when I use Android Pay on the vending machines it will always authorize $1.50 and then a couple days later it will charge for the actual price when I view my credit card transactions.