Your question doesn't make sense. If your wife is contributing to an HSA while on Medicare, she is disqualified, and the contributions are not tax deductible, plus are subject to an additional 6% penalty per year.
Please know that an HSA is an individual account, there are no joint HSAs. If your wife is covered by Medicare but you have a qualifying HDHP medical plan and are not covered by Medicare, then you can contribute to an HSA in your name without any problems, but your wife can't contribute to an HSA in her name. (Your wife's Medicare does not disqualify your contributions to your own HSA.)
We can't see your tax returns so we can't see what you are doing. In the HSA section, you need to very carefully answer the question about what kind of medical insurance you have for each spouse (individual HDHP, family HDHP, Medicare, or something else). And, you need to make sure any HSA contributions are being allocated under the name of the correct account owner.
