If you have legitimate records and documents for all the information on your tax return(s), even if the IRS ever questioned your return, you would be able to show proof why you filed the way you did.
Yes, the fact that it's been more beneficial to file Married Filing Separately (MFS) versus Married Filing Jointly (MFJ) is unusual. Generally, filing jointly (one tax return instead of two) will give you a bigger refund or less taxes due.
Perhaps your refund is $3,000 more filing MFJ versus MFS because when you file MFS, your tax rate is higher and you won't be able to claim:
If you file MFS and live in Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington, or Wisconsin, you have to deal with community property allocations and adjustments, which adds extra work and complexity to your taxes.
The main reason you'd want to file MFS is to protect yourself from inaccurate tax information reported by your spouse, or in cases where your spouse refuses to file a joint return (or refuses to file, period) and you don't want to get in trouble.
When you file MFS, your refund can't be seized to pay off your spouse's debts. However, filing jointly as an innocent or injured spouse can head off refund seizures as well.
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