We have transferred the payment due to ~ company to your company by mistake.
We apologize for the inconvenience, but could we ask you to transfer back this money to us?
ご質問ありがとうございます。
"We have transferred the payment due to ~ company"=「〇社に送金するはずであった支払いを~に送金しました」
"to your company by mistake."=「誤って御社に。」
"We apologize for the inconvenience"=「お手数をおかけして申し訳ありません」
"but could we ask you to transfer back this money to us?"=「が、その支払いを弊社に送金していただけないでしょうか。」
ご参考に!