The best way to deal with this situation is to contact the customer (they would not be considered as your employer) and figure it out. Get them to file a corrected 1099-MISC if needed. 

If that is not possible, you can report what you feel is the proper amounts, in which case you will need to attach a statement addressing the change in the way you reported the 1099-MISC and you must be ready to supply documentation to support your case when the IRS inquires about it. 

You will need to print and paper file (mail) your return with an extra explanatory statement.  

Again, I would contact the person/entity that filed the 1099-MISC. Explain that you are going to dispute the 1099-MISC they issued and that because of this the IRS will scrutinize both your books and their's. It could be an honest error in which case they will simply issue a corrected 1099-MISC. 

https://pocketsense.com/dispute-amount-1099-misc-8373403.html

https://ttlc.intuit.com/replies/5442014

How do I attach a statement, when I'm filling my taxes with Intuit turbotax? I got an incorrect 1099-NEC and the company who issue it , is out of bussiness now. 

You can't attach statements if you e-file.   You would need to file by mail to include attachments, but the IRS doesn't want attachments.   @cjsuarez 

What is the problem with your 1099-NEC?  

I did a job for a company. They sent a micro-deposit confirmation on my bank account, but never the payment for the job, even when I sent them several messages. Eventualy they stopped answering. Now they send me a 1099-NEC for a payment I never got.  I left messages at the phone that appears on the form but nobody returns the call. I don't want to pay taxes for money I didn't received. Is there a way I can void the 1099-NEC received?

I did a job for a company. They sent a micro-deposit confirmation on my bank account, but never the payment for the job, even when I sent them several messages. Eventualy they stopped answering. Now they send me a 1099-NEC for a payment I never got.  I left messages at the phone that appears on the form but nobody returns the call. I don't want to pay taxes for money I didn't received. Is there a way I can void the 1099-NEC received?

Yes, enter only the income you actually received.  Keep your 1099-NEC in your file with your notes and documentation showing you never received the money, as well as your steps to obtain a correction.  The IRS does not require you to report income you never received. 

If you like you can report this company to the IRS by using Form 3949-A to report suspected tax law violations. You certainly do not have to use this but it's an option to provide information to them about this company. Click the form and instructions are included.