The Direct Debit VAT payments are usually collected automatically from your bank account 3 working days after the payment deadline on your VAT return.
There appears to have been some issues with the transfer of Direct Debits, having failed in some cases. Firstly make sure that the 3 working days have passed. Before you make a payment, it’s best that you contact HMRC, to avoid double paying. Make sure you have all of the necessary information gathered. You can call the VAT helpline to check your records. There shouldn’t be any penalties in a situation like this.