Multiple Payments
You can't be charged twice for the same upgrade. Both stores block it.
Apple won't let the same Apple ID buy the same paid app or non-consumable in-app purchase twice. If you try, the App Store offers a free re-download instead.
Edge cases that look like a double charge
Seconds and Seconds Pro
They're different products, so Apple treats them as separate purchases. If you bought both by mistake, request a refund from Apple for whichever one you don't want.
Different Apple IDs
Purchases don't transfer between Apple IDs. Buying on a second Apple ID is a second purchase, not a duplicate.
Check your purchase history on each Apple ID to confirm where the charges came from.