Payment for self assessment

Hi! Recently completed a self assessment for 23-24 due to having additional income outside my salaried role, more than my tax free allowance. I've been paying more tax through my tax code this year (since March 2023). The tax code notice has the correct additional income noted, and so my tax code seems sensible. I was still also asked for payments in January 2024 and July 2024, which I thought were to cover the tax year 23-24, with any balancing payment for the year due in January 2025. From my calculations, I think I have potentially therefore paid too much tax, due to paying both through my tax code, and through the self assessment service. The 2k odd I've paid in two lump sums doesn't seem to be reflected anywhere in the calculation as far as I can see, the calculation only has the value from my P60. Is there a risk I'm paying the tax twice? In addition to that, having completed my self assessment in the calculation they have added a student loan repayment to my income tax due. I have been paying my student loan through my employer - is this amount added just the difference owed? The calculation doesn't have any other student loan value included, although I submitted the amount paid through my payslip during the process. Is this just the difference? Will this go to the student loan company?

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