I made a pension contribution from my company to a personal pension as an Employer Contribution and recorder this as a bank payment to the Pension code in Payroll with the VAT code as Exempt. When I run my VAT return this shows as an additional purchase expense. Is that correct?
I would suggest using the No VAT code instead but either way it is an expense. The inclusion of it on the VAT return is not going to affect the amount of VAT you owe but will change the value of box 7, a large amount suddenly appearing there may alert HMRC's computers to query the return if it looks different to a "normal" return.