Qubits in topological quantum computation are built from non-Abelian anyons. Adiabatic braiding of anyons is exploited as topologically protected logical gate operations. Thus, the adiabaticity upon which the notion of quantum statistics is defined plays a fundamental role in defining the non-Abelian anyons. We study the nonadiabatic effects in braidings of Ising-type anyons, namely, Majorana fermions in topological superconductors, using the formalism of time-dependent Bogoliubov-de Gennes equations. Using this formalism, we consider nonadiabatic corrections to non-Abelian statistics from (1) tunneling splitting of anyons imposing an additional dynamical phase to the transformation of ground states and (2) transitions to excited states that are potentially destructive to non-Abelian statistics since the nonlocal fermion occupation can be spoiled by such processes. However, if the bound states are localized and being braided together with the anyons, non-Abelian statistics can be recovered once the definition of Majorana operators is appropriately generalized taking into account the fermion parity in these states. On the other hand, if the excited states are extended over the whole system and form a continuum, the notion of local fermion parity no longer holds. We then quantitatively characterize the errors introduced in this situation.