Fluctuation relations establish rigorous identities for the nonequilibrium averages of observables. Starting from a general transport master equation with time-dependent rates, we employ the stochastic path integral approach to study statistical fluctuations around such averages. We show how under nonequilibrium conditions, rare realizations of transport observables are crucial and imply massive fluctuations that may completely mask such identities. Quantitative estimates for these fluctuations are provided. We illustrate our results on the paradigmatic example of a mesoscopic RC circuit.