TurboTax would think that you have two HSAs only because you told TurboTax that you had two HSAs.
Are you filing married joint? Do both you and your spouse have W-2s with a W in box 12? (This would indicate contributions to HSAs. If you did this, TurboTax would ask in each case to whose HSA the code W contribution went, thus making the chance for you to accidently indicate that you each had an HSA).
In the HSA interview, did you go through questions for you and your spouse? These would be separate sections. This should not happen if you didn't tell TurboTax about two HSAs.
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