When developers gain thorough understanding and knowledge of software security, they can produce more secure software. This study aims at empirically identifying and understanding the security issues posted on a random sample of GitHub repositories. We tried to understand the presence of security issues and their key themes and topics. We applied a mixed-methods approach, combining topic modeling techniques and qualitative analysis. Our findings have revealed that a) the rate of security-related issues was rather small (approx. 3% of all issues), b) the majority of the security issues were related to identity management and cryptography topics. We present 7 high-level themes of problems that developers face in implementing security features.