A form 1099-MISC is additional taxable income. There is usually no tax withheld on a 1099-MISC. If you add income with no additional withholding, naturally your refund will be reduced because you have to pay tax on the 1099-MISC income. If the 1099-MISC is self-employment income (in box 7) you have to pay self-employment tax as well as income tax.
You can file separately, but unless you live in Ohio, you will almost certainly pay more tax altogether than if you file jointly.
