Does my employer have rights to accuse of FMLA fraud?

I'm not sure what your employer is exactly accusing you of. FMLA leave is either allowed or disallowed depending on your eligibility and condition. If your physician has certified the need for the leave, the employer cannot disregard the certification, but can seek a second opinion. If that medical opinion differs from that of your doctor, the employer may require a third deciding opinion from a neutral medical provider. Now if you took leave that wasn't supported by a doctor's certification or engaged in activities inconsistent with your medical condition, the employer may or may not be justified in imposing discipline. More information is needed to give a more definite answer.