Package registries host reusable code assets, allowing developers to share and reuse packages easily, thus accelerating the software development process. Current software registry ecosystems involve multiple independent stakeholders for package management. Unfortunately, abnormal behavior and information inconsistency inevitably exist, enabling adversaries to conduct malicious activities with minimal effort covertly. In this paper, we investigate potential security vulnerabilities in six popular software registry ecosystems. Through a systematic analysis of the official registries, corresponding registry mirrors and registry clients, we identify twelve potential attack vectors, with six of them disclosed for the first time, that can be exploited to distribute malicious code stealthily. Based on these security issues, we build an analysis framework, RScouter, to continuously monitor and uncover vulnerabilities in registry ecosystems. We then utilize RScouter to conduct a measurement study spanning one year over six registries and seventeen popular mirrors, scrutinizing over 4 million packages across 53 million package versions. Our quantitative analysis demonstrates that multiple threats exist in every ecosystem, and some have been exploited by attackers. We have duly reported the identified vulnerabilities to related stakeholders and received positive responses.