Pension Contributions Reporting and Potential Tax Overpayment

I am competing a SA for the first time and struggling with declaring pension information. I think I have done properly but has an unexpected tax calculation resulting in an overpayment by me. There is nothing else complicated on tax return other than £6,250 of dividend income. I have a defined benefit work scheme where my employer pays my pension, and in 2023-24 they made no contributions to it. I did pay in £17,000 in AVC contributions but I understand I do not include this amount these are taken from pay before tax calculation - so no relief is due, I also opened a SIPP in 2023-24 where I contributed £33,000 and my provider claimed £8,250 20% tax relief. As per SA guidance I added £41,250 in box 1. In the tax calculation is states "Your pension payments of £41,250.00 have increased your Scottish basic rate limit.". This means a pay less tax on income although I already received £8,250 from my SIPP provider. This has resulted in a stated overpayment of nearly £5000. Is this correct how SIPP contributions raise the basic rate tax element?

Hi,
Though your calculation is most likely correct, your overpayment is almost certainly the higher rate relief due from your pension contributions, we would need to review your calculation to confirm this for you. You will need to contact our Self Assessment team to confirm this.
Self Assessment: general enquiries
Thank you.