Why am I being double charged for Shopify fees?

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Hi team, I’ve been using Shopify for a number of years and recently received an email to say we have a negative balance of over £500 that we must pay due to an accumulation of Shopify fees. 

I’ve looked into this and looked at many example orders and can see that when we receive a customer order we receive a gross amount, for example £500, Shopify then apply their fees - £30 then £470 is paid into our business account. Therefore, Shopify have taken the £30 fee already. This fee then gets added as a negative balance to the fees total. 

Now Shopify are asking me to pay the fees total balance of £500+ yet they have not paid these fees to us during payouts, they have already taken it. 

This seems very strange and Shopify now want us to pay the negative balance of fees, yet the money was deducted already before they paid into our account. 

Why has this only been flagged now after being with them for a number of years, nothing has changed our side and we don’t want to double pay. 

Has anyone else had this issue, what was the cause and how was it resolved?

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