Microcontroller systems are integral to our daily lives, powering mission-critical applications such as vehicles, medical devices, and industrial control systems. Therefore, it is essential to investigate and outline the challenges encountered in developing secure microcontroller systems. While previous research has focused solely on microcontroller firmware analysis to identify and characterize vulnerabilities, our study uniquely leverages data from the 2023 and 2024 MITRE eCTF team submissions and post-competition interviews. This approach allows us to dissect the entire lifecycle of secure microcontroller system development from both technical and perceptual perspectives, providing deeper insights into how these vulnerabilities emerge in the first place. Through the lens of eCTF, we identify fundamental conceptual and practical challenges in securing microcontroller systems. Conceptually, it is difficult to adapt from a microprocessor system to a microcontroller system, and participants are not wholly aware of the unique attacks against microcontrollers. Practically, security-enhancing tools, such as the memory-safe language Rust, lack adequate support on microcontrollers. Additionally, poor-quality entropy sources weaken cryptography and secret generation. Our findings articulate specific research, developmental, and educational deficiencies, leading to targeted recommendations for researchers, developers, vendors, and educators to enhance the security of microcontroller systems.