Vat error on imported goods

Just discovered that my VAT returns for several previous quarters shows VAT on my EU supplier invoices. The original invoices do not show VAT but… when entering them onto the system it defaults to 20% but then shows in red “EC Exempt” which then cancels the VAT so that the end figure shows the original net figure. However, I am told this is wrong because the VAT liability is still showing in BOX 2. This means in effect that I have charged myself VAT…is this correct? If so…how do I roll back VAT returns which don’t give me that option to correct

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