Do active military members have a limit to how much they can contribute to the ROTH IRA? How do I stop the system from falsely flagging my contribution?

Military members can contribute to a Roth IRA or a Traditional IRA if they are eligible based on their income, filing status and having a retirement plan at work.

Contributions to a Traditional IRA when you have a retirement plan at work - https://www.irs.gov/retirement-plans/plan-participant-employee/2024-ira-contribution-and-deduction-limits-effect-of-modified-agi-on-deductible-contributions-if-you-are-covered-by-a-retirement-plan-at-work

Roth IRA contributions are not tax deductible

Contributions to a Roth IRA based on your filing status and income - https://www.irs.gov/retirement-plans/plan-participant-employee/amount-of-roth-ira-contributions-that-you-can-make-for-2024

How much did you contribute?  Are you sure you have a IRA?  Does it come out of your paycheck?  If it's a different kind of IRA like though the employer then you only enter it from the W2 and not under Deductions as a contribution.