We analyze Allen-Cahn functionals with stationary ergodic coefficients in the regime where the length scale $δ$ of the heterogeneities is much smaller (microscopic) than the interface width $ε$ (mesoscopic). In a companion paper, we show that if the ratio $ε^{-1} δ$ vanishes fast enough as $ε\to 0$, then the functionals converge to an effective surface energy where the energy density is determined by homogenization effects originating at microscopic scales. Here we prove that if the ratio $ε^{-1} δ$ vanishes too slowly, the limit of the functional may actually be smaller than this homogenized energy. We refer to this as the rare events regime. In the case of the random checkerboard in dimension one, we use large deviations techniques to give a complete description of the rare events regime, showing that the limiting energy depends in a nontrivial way on the limit of $ε^{-1} δ| \log ε|$. We further construct, in any dimension, examples of random media in which rare events become relevant at algebraic scales $δ\approx ε^{1 + α}$ for an arbitrary $α> 0$, as well as almost periodic examples in which atypical configurations play the same role as rare events.