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We investigate the quasiparticle dynamics in the prototype heavy fermion CeCoIn$_5$ using ultrafast optical pump-probe spectroscopy. Our results indicate that this material system undergoes hybridization fluctuations before full establishment of the heavy electron coherence, as the temperature decreases from $\sim$120 K ($T^\dagger$) to $\sim$55 K ($T^*$ ). We reveal that the observed anomalous phonon softening and damping reduction below $T^*$ are directly associated with opening of an indirect hybridization gap. We also discover a distinct collective mode with an energy of $\sim$8 meV, which may be the experimental evidence of the predicted unconventional density wave. Our observations provide critical informations for understanding the hybridization dynamics in heavy fermion materials.