It is normal that your refund decreased when you add your file 1099-MISC. Income reported on a form 1099-MISC is self-employment income which is subject to self-employment tax of 15.3% in addition to income tax. Moreover, there is generally no tax withheld on a form 1099-MISC which further reduces your refund.
This said, you should still file jointly as most couples find it more beneficial to file jointly. Filing separately subjects you to higher rates and will make you ineligible for a number of tax credits such as the Earned Income Tax credit.
Please read this TurboTax FAQ for more information:
https://ttlc.intuit.com/replies/3288477
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