Self-assessment was received but not applied

Hello, I submitted my self-assessment more than 3 weeks ago. I received the confirmation e-mail from HMRC and checked via my account that the self-assessment was received. According to my self-assessment, I had to pay the tax due. When I checked several days later, no tax was due on my summary page, but I decided to pay it anymore. Now, I can see that my account is still in credit and HMRC still offers me repayment options. However, if I follow the link to view my last submitted tax return and check my calculation, I can see the sum due is equal to the amount I paid (and the amount of my account is in credit now). What can be a reason for this discrepancy? When can I expect it might be resolved? Am I subject to a late self-assessment submission penalty in that case? Thank you.

Hi,

You will need to contact our Self Assessment team so we can access your record to review this for you.

Self Assessment: general enquiries

Thank you.