Recent experiments on CdSe nanoplatelets synthesized with precisely controlled thickness that eliminates ensemble disorder have allowed accurate measurement of quantum coherence at room temperature. Matching exactly the CdSe cores of the experimentally studied particles and considering several defects, we establish the atomistic origins of the loss of coherence between heavy and light hole excitations in two-dimensional CdSe and CdSe/CdZnS core/shell structures. The coherence times obtained using molecular dynamics based on tight-binding density functional theory are in excellent agreement with the measured values. We show that a long coherence time is a consequence of both small fluctuations in the energy gap between the excited state pair, which is much less than thermal energy, and a slow decay of correlation between the energies of the two states. Anionic defects at the core/shell interface have little effect on the coherence lifetime, while cationic defects strongly perturb the electronic structure, destroying the experimentally observed coherence. By coupling to the same phonon modes, the heavy and light holes synchronize their energy fluctuations, facilitating long-lived coherence. We further demonstrate that the electronic excitations are localized close to the surface of these narrow nanoscale systems, and therefore, they couple most strongly to surface acoustic phonons. The established features of electron-phonon coupling and the influence of defects, surfaces, and core/shell interfaces provide important insights into quantum coherence in nanoscale materials in general.