Filing a tax return is the way to pay the correct amount of tax. If you did not withhold enough, you will have to pay the difference when you file your tax return.

If I understand your question, you made $15,000 and had $1,000 in tax withheld. If that's the case, you should still get a refund.

no, he made 15K but his w2 only lists 900 as his federal taxable income.  Is his w2 wrong and if so what do I do given there is no time to fix it and if it is correct, then how to I make sure he pays taxes on the $15K and not the $1K

What is in Box 1 of his W-2? If it is $15,000, remember that he is entitled to a standard deduction, even as a dependent. if the amount in Box 1 is incorrect, you will need a corrected W-2. The amount that is entered on the tax return must match what the IRS receives.

Dependents – If you can be claimed as a dependent by another taxpayer, your standard deduction for 2020 is limited to the greater of: (1) $1,100, or (2) your earned income plus $350 (but the total can't be more than the basic standard deduction for your filing status). Single under age 65-$12,400.

If his employer was changing payroll systems maybe he should have another W2.  Or ask the employer.  Or did he put the difference into a 401K plan?  Check W2 box 12.

I finally got a hold of his employer and they acknowledged that they completed his W2 wrong so they are going to reissue it ... not until after the 17th, but I'm just using the correct numbers anyway.

You can file an amendment and pay any tax that may be due before 05/17/21.   If you e-file now before the company issues the corrected information, it may cause a serious delay in processing the return as the information is not going to match.  

You can get an extension by paying all or part of your estimated income tax due and indicate that the payment is for an extension using Direct Pay, the Electronic Federal Tax Payment System (EFTPS), or a credit or debit card. This way you won’t have to file a separate extension form and you will receive a confirmation number for your records.

If you prefer to e-file the form, you can do that with TurboTax Easy Extension.    It's the fast, easy, and secure way to e-file your federal tax extension.   But the option above is better.