I don't believe this is a software problem. TurboTax will take the information you entered from your employer's Form W-2 to complete Form 8880. Check Box 12, Code D, which displays amounts you contributed to your employer's retirement plan. If this number does not reflect your actual contribution, then contact your employer's payroll department and request a Corrected W-2.
Click this TurboTax FAQ What is a Form W-2? for more information.
