Even if the agency considers you an independent contractor, they should issue you a 1099 or at the very least be willing to give your their EIN number so you can report your income. You can certainly attempt to e-file with 99-9999999, but you may get an e-filing error. But it may go through. And no, if it goes through, it is not going to cause an issue with the IRS, because they have nothing reported to them for the income. You are reporting it according to their instructions after all. Do they issue you anything when they make the payments that might have their tax ID number on it?
See this discussion, where Barbara outlines the steps needed to report the IHSS income for the purposes of claiming the EIC and CTC as well as negating the entry to report the income as non-taxable. I think this is what you have done, but there are links in her answer that reference that you are reporting it correctly. I think the issue now is getting the return e-filed so you are not relegated to filing by mail. @allimacsnwod
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