Application is "Online Rejected" - will I incur late fee?

I submitted my Self Assessment weeks ago, it was confirmed as received. When I submitted, the site told me I would owe some money. However even weeks later, my tax account online says I owe no tax, so I have no option to pay. I called up HMRC and the person on the phone said my application was "Online Rejected" so she would refer it to a team to investigate -- which may not be done until April 2024. She said I might incur a late fee as a result, which I could then appeal. Two questions: 1. I believe it's possible to pay without signing in. Should I just pay the amount my return shows, in the hope that's the right amount and I don't get a late fee? I don't believe I can pay "on account" since I'm not a business user. 2. Has anyone else run into this before and have any advice? Thanks.

Hi,
You can make a payment before your tax return has been processed.
All online payment options are available by selecting the 'pay now' button on our website:
Pay your Self Assessment tax bill
If you have An amount calculated when you submtted the tax return then you can pay that amount.
Thankyou.