See a professional tax preparer. You may have a great deal of issues to work out.
When you are an LLC with no employees, you have the option of using your SSN or getting a federal EIN (employer ID number). When you have employees, you must have an EIN. Did you get one?
You must withhold federal and state income taxes, social security and Medicare Tax, did you do that?
You must file form 941 quarterly with the IRS to report the federal withholding and federal unemployment tax payments, did you do that? There will be a similar quarterly form for your state taxes withheld.
You must issue each employee a W-2 at the end of the year, and when you file the W-2, a copy goes to the IRS, along with a W-3 form that summarizes all your employee W-2s. Did you file those documents?
It kind of sounds like you didn't, if the IRS says they have no records of the employees' wages. Aside from causing hardship to your employees, failing to do these tasks can subject you to large penalties.
You may also have significant state responsibilities. For example, in New York State, an employer must provide each employee with a pay statement or pay stub containing 15 specified items of information, and fine for noncompliance is $100 per paycheck per employee.
If these were subcontractors, you can forget about all the withholding and pay stub talk, but you must issue each subcontractor a 1099-NEC no later than January 31, with copies to the IRS.
Good luck.
