A customer of ours initiated a chargeback against an order that had already been refunded. Why doesn't Shopify protect its merchants from this type of potential fraud by filing disputes for lack of grounds on behalf of the merchant?
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I'm sorry to hear you got a chargeback. Shopify's payment system is handled by Stripe, so it's really up to Stripe to dispute the chargeback on your behalf. As you have already mentioned that you have already refunded the order, you should not have an issue resolving the case quickly and even have your chargeback fees In any, refunded.
If you refunded only after receiving the chargeback, then it could cause issues with the case and you often will have to let the payment gateway provider know that you are willing the close the case by refunding them. Most chargeback cases can take up to 1 week to resolve.
In addition, Shopify has a basic fraud analysis. I recommend you look into that if you haven't, yet.