Since you have determined by using the worksheet in IRS Publication 571 that the additional $3000 contribution for your wife's service is allowed, then you can safely ignore the warning in TurboTax and it will not trigger errors that will disallow filing, nor will it generate any forms for penalties of overcontribution.
The screen "Let's Check Your Retirement Contributions" in TurboTax does say that "The maximum most people under age 50 can contribute to all salary deferral retirement plans for 2025 is $23,500". On that same screen, there is guidance on what to do if the total contribution is above the allowable amount under the "What Steps Do I Need to Take?" link
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