Lagrangian Particle Dispersion modeling (LPDM) is a useful tool for understanding atmospheric transport pathways and the origin of air masses sampled during field campaigns. Observations of CO2 and CH4 from an aircraft platform were made during 2020-2022 over Uganda, a region of complex circulation and large convection, seasonally. To aid interpretation of these observations,, we simulated 10-day backward trajectories for a subset of observations using the HYSPLIT model. A significant anomaly occurred toward the end of the simulation (May 25 - May 27, 2021, 8-10 days prior to the observation point), where more than half of the 500 simulated particles, predominantly located between 2500m and 5000m AGL, exhibited a severe violation of mass conservation. Our objective is to elucidate the specific atmospheric dynamics responsible for this mass conservation violation event. We investigate synoptic weather charts and meteorological reanalysis data for May 25-27, 2021, focusing on vertical velocity fields, divergence, and convective indices over the regions indicated by the early stages of the back trajectories, to determine the root cause of the observed model behavior. Understanding these limitations is crucial for interpreting trajectory results in dynamically active regions.