Tax withholding is an estimation, usually taxpayer file a W-4 with employer to tell them how much to withhold.
IRS knows it's an estimation so if for the first year your actual tax is more than $500 over the withheld tax, there is no penalty. And you should adjust your W-4 for the next year.
If second year you keep having this problem (>$500), then you have to pay a penalty. Detail of calculation is on your tax form.
So is this your first year that you have to pay more than $500 in tax return?