The rapid evolution of drone technology has introduced unprecedented challenges in security, particularly concerning the threat of unconventional drone and swarm attacks. In order to deal with threats, drones need to be classified by intercepting their Radio Frequency (RF) signals. With the arrival of Sixth Generation (6G) networks, it is required to develop sophisticated methods to properly categorize drone signals in order to achieve optimal resource sharing, high-security levels, and mobility management. However, deep ensemble learning has not been investigated properly in the case of 6G. It is anticipated that it will incorporate drone-based BTS and cellular networks that, in one way or another, may be subjected to jamming, intentional interferences, or other dangers from unauthorized UAVs. Thus, this study is conducted based on Radio Frequency Fingerprinting (RFF) of drones identified to detect unauthorized ones so that proper actions can be taken to protect the network's security and integrity. This paper proposes a novel method-a Composite Ensemble Learning (CEL)-based neural network-for drone signal classification. The proposed method integrates wavelet-based denoising and combines automatic and manual feature extraction techniques to foster feature diversity, robustness, and performance enhancement. Through extensive experiments conducted on open-source benchmark datasets of drones, our approach demonstrates superior classification accuracies compared to recent benchmark deep learning techniques across various Signal-to-Noise Ratios (SNRs). This novel approach holds promise for enhancing communication efficiency, security, and safety in 6G networks amidst the proliferation of drone-based applications.