If the bank pulled what they thought you would be taxed on the self-employment income and put that into a separate account, you would report the income the same way as if that never happened.
Repot the full amount as income and also report your expenses.
I am assuming you are a Sole-Proprietorship for tax purposes and file Schedule C to report your self-employment income.
I also assume you instructed the bank to do the allocation to a separate account since it is not a bank's duty to withhold taxes from your deposits.
Again, taxes not paid on unemployment would be your tax liability and calculated on your federal return.
There is no opportunity to put the blame on the state even if you had asked when you applied.
Compute the 2024 return and see if a penalty is assessed. You may not need to worry about it for 2024, but 2025 might be a different story so you might want to start making those estimated tax payments for 2025.
According to the IRS:
"You may avoid the Underpayment of Estimated Tax by Individuals Penalty if:
- Your filed tax return shows you owe less than $1,000 or
- You paid at least 90% of the tax shown on the return for the taxable year or 100% of the tax shown on the return for the prior year, whichever amount is less. If your adjusted gross income (AGI) for 2023 was more than $150,000 ($75,000 if your filing status for 2024 is married filing separately), substitute 110% for 100%."
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