To this day, von Neumann definition of entropy remains the most popular measure of quantum entanglement. Much of the literature on entanglement entropy, particularly in the context of field theory, has focused on isolating the UV divergences. Zero-mode divergences of the entanglement entropy are less studied in this context, and apart from being easier to isolate, they offer an interesting insight into the physics of the system. To gain a better understanding of the system in this limit, we develop the free particle approximation of Harmonic oscillator, with which we investigate the properties of entropy divergence in continuous bi-partite quantum systems such as the coupled Harmonic oscillators and the Hydrogen atom. We also show zero-mode divergence of the entropy of environment-induced entanglement in a tri-partite oscillator system. We discuss the implications of our result for field theory and IR structure of gravity.