Multiple charges on a credit card
When you place an order, you will see an initial charge that simply verifies the account. This money is not actually taken from your account, because this is not an actual charge; payment only goes through after your order is into shipping preparation. The amount may also change very slightly due to daily-changing yen exchange rates between the time of the verification and the time of the final purchase.
Every time you merge or edit your order, your card may show another charge each time–but rest assured, you were not actually charged twice or more. Your initial charge(s) will be refunded eventually, but it might take a little time for your account to display these changes.
As stated, the initial charges are all verification charges that will eventually disappear or be canceled. There is only one final charge that actually goes through, and this happens when the order is shipped. Sometimes it takes the bank a long time–maybe even until the following month’s statement–to show the updated information.