This paper presents a technique to cope with the gap between high-level planning, e.g., reference trajectory tracking, and low-level controlling using a learning-based method in the plan-based control paradigm. The technique improves the smoothness of maneuvering through cluttered environments, especially targeting low-speed velocity profiles. In such a profile, external aerodynamic effects that are applied on the quadrotor can be neglected. Hence, we used a simplified motion model to represent the motion of the quadrotor when formulating the Nonlinear Model Predictive Control (NMPC)-based local planner. However, the simplified motion model causes residual dynamics between the high-level planner and the low-level controller. The Sparse Gaussian Process Regression-based technique is proposed to reduce these residual dynamics. The proposed technique is compared with Data-Driven MPC. The comparison results yield that an augmented residual dynamics model-based planner helps to reduce the nominal model error by a factor of 2 on average. Further, we compared the proposed complete framework with four other approaches. The proposed approach outperformed the others in terms of tracking the reference trajectory without colliding with obstacles with less flight time without losing computational efficiency.