Oxygen vacancies in the MgO barriers of epitaxial Fe/MgO/Fe magnetic tunnel junctions are observed to introduce symmetry-breaking scatterings and hence open up channels for noncoherent tunneling processes that follow the normal WKB approximation. The evanescent waves inside the MgO barrier thus experience two-step tunneling, the coherent followed by the noncoherent process, and lead to lower tunnel magnetoresistance, higher junction resistance, as well as increased bias and temperature dependence. The characteristic length of the symmetry scattering process is determined to be about 1.6 nm.