A Form 1099-NEC can report income tax withholding, so if the Form 1099-NEC shows what was withheld, there is no problem (as long as the company actually sent the withheld income tax to the Treasury). If the company withheld Social Security and Medicare taxes as well, they apparently considered you to be an employee and should have sent you a W-2, not a Form 1099-NEC. It's not legal for them to simply withhold taxes and keep the money.
The more basic question is whether or not you were an independent contractor or an employee under the law:
https://www.irs.gov/businesses/small-businesses-self-employed/independent-contractor-self-employed-o...
