Towards sixth-generation networks (6G), satellite communication systems, especially based on Low Earth Orbit (LEO) networks, become promising due to their unique and comprehensive capabilities. These advantages are accompanied by a variety of challenges such as security vulnerabilities, management of hybrid systems, and high mobility. In this paper, firstly, a security deficiency in the physical layer is addressed with a conceptual framework, considering the cyber-physical nature of the satellite systems, highlighting the potential attacks. Secondly, a learning-driven detection scheme is proposed, and the lightweight convolutional neural network (CNN) is designed. The performance of the designed CNN architecture is compared with a prevalent machine learning algorithm, support vector machine (SVM). The results show that deficiency attacks against the satellite systems can be detected by employing the proposed scheme.