It depends. It is very rare that Married Filing Separately produces an overall better tax result than Married Filing Joint, but it can happen on occasions. When it does happen, it would be because of itemized deductions, perhaps being able to take advantage of lower separate threshholds for unreimbursed business expenses (deductions subject to 2% of AGI threshhold), or medical deductions (subject to 7.5% of itemized threshhold). At times, when one spouse has a large amount of these types of deductions, filing separately does result in an overall lower taxable amount because more deductions can be obtained.
Having said this, however, there is a caution. Remember that if you file as separately, and one spouse itemizes, both spouses must claim itemized deduction. It is not impossible that inputting information into the system can produce a false result if one spouse is claiming all of the itemized deductions available, and then, on the other spouse's return, the standard deduction is being claimed. If you have itemized on your return, make sure on your spouse's return it is marked as my spouse itemized deductions. (Itemized deductions include claiming your home mortgage interest, real estate taxes, and other similar deductions. The following FAQ has more information on this): https://ttlc.intuit.com/replies/3302313
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