We use simulations to examine hysteresis and noise in a model system that produces heterogeneous orderings including stripe and clump phases. In the presence of a disordered substrate, these heterogeneous phases exhibit 1/f α noise and hysteresis in transport. The noise fluctuations are maximal in the heterogeneous phases, while in the uniform phases the hysteresis vanishes and both α and the noise power decrease. We compare our results to recent experiments exhibiting noise and hysteresis in high-temperature superconductors where charge heterogeneities may occur.