Hi, Khurram!
Your Shopify subscription can only be charged to the payment method on file under Settings > Billing. Depending on your location, you may be able to pay for your Shopify subscription using a credit card or co-branded debit card, Shopify Balance, or PayPal. ACH debits are only supported for stores in the United States on the Shopify Plus plan.
Have you received any emails from Shopify regarding the charges you noticed on your Wise account?