The rich nature of van der Waals interactions between artificially-stacked atomic layers has been demonstrated by various quantum states and resonant tunneling transport in low-dimensional materials. However, the role of topological fluctuations in quantum transport through artificially-stacked junctions of 2D superconducting materials, and the resulting energy dissipation, remain elusive. In this research, unique phase-slip centers are designed in artificially-stacked junction areas, where nonequilibrium quasiparticles are formed and relaxed with energy dissipation. The phase slips are observed as voltage steps (peaks or valleys) in transport measurements across a junction between two exfoliated NbSe2 flakes, and at a distance of 4 μm from the junction using local and nonlocal chemical potential probes. Accordingly, two types of energy dissipation modes are newly identified in the artificially-stacked NbSe2 when subjected to an in-plane magnetic field, which implies distinct vortex formation and current flow in the superconducting junction under magnetic fields.