Your second w-2 may have put you into a higher tax rate bracket . Your employer was only withholding based on the knowledge that was the only income you received that year so withheld at a lower rate than you were actually subject too. Do note a that a refund is a tax-free loan to the IRS. You may want to have less withheld and invest the savings... Or many use it as forced savings but it is not the best financial strategy.
I hope this helped. Good luck.