Don't worry, you just need to file an amended return to change the federal withholding on your w-2 form. 

Follow the directions in the TurboTax FAQ below to prepare an amended return.

https://ttlc.intuit.com/replies/3288565

Note: You are required to mail your amended return. This type of return is not eligible for e-file.

Will they send a bill for the refund once they process the amended return? Penalties?

No, you must pay the difference in the refund amount and mail the payment with your amended return. The balance due will be listed on line 20 of your amended return Form 1040X.

As long as you mail your amended return and payment by 04/15/2019, you will not owe any fines or penalties.