Generally, if you look at your bank statement or even scroll through your history of banking activity, you will be able to figure out the amount that is personal vs the amount that is for a rental property. You will just enter this amount without the 1099-INT as if you had one.
The reason TurboTax is telling you that, is in many situations, when you are married, you make out better when you file jointly. This is because many credits are limited or not available for filing separately, and things like Social Security become 85% taxable automatically regardless of income. So, it is possible that your situation will be different and you would be better off filing a separate return, so, the best thing to do is to run the numbers both ways and then compare the results.
If you are using the desktop version, you can use the What If form. If you are using the online version, you can just create a dummy account to avoid entering and deleting the information multiple times.
Married Filing Joint versus Separate
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