Don't worry! You didn't get double charged.
The way that Apple manages subscription changes is a little wonky!
You will see a charge for the full cost of two Pro Subscriptions, but you will receive a refund from Apple for the pro-rated amount on the first site.
ex. You have had one Pro Site Subscription for a 6 months, then added a second Pro Site Subscription. You will see a charge for the full price of two sites $240 (+tax). You will then get a refund for $60 (the pro-rated refund for the unused portion of your first subscription)