Under normal circumstances, after the tax authorities (national tax authorities) pay taxes on behalf of invoicing, at the time of declaration, the amount paid on behalf of invoicing should be filled in the second line "Among them, the tax-free sales of VAT invoiced by tax authorities", and the tax paid on behalf of invoicing should be filled in the eleventh line "Current tax payable minus the amount collected", which is no problem.

As for your repeated deduction, I guess you haven't paid the tax in line 11.

I suggest you explain the situation to the tax authorities and apply for tax refund.