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The package manager (PM) is crucial to most technology stacks, acting as a broker to ensure that a verified dependency package is correctly installed, configured, or removed from an application. Diversity in technology stacks has led to dozens of PMs with various features. While our recent study indicates that package management features of PM are related to end-user experiences, it is unclear what those issues are and what information is required to resolve them. In this paper, we have investigated PM issues faced by end-users through an empirical study of content on Stack Overflow (SO). We carried out a qualitative analysis of 1,131 questions and their accepted answer posts for three popular PMs (i.e., Maven, npm, and NuGet) to identify issue types, underlying causes, and their resolutions. Our results confirm that end-users struggle with PM tool usage (approximately 64-72%). We observe that most issues are raised by end-users due to lack of instructions and errors messages from PM tools. In terms of issue resolution, we find that external link sharing is the most common practice to resolve PM issues. Additionally, we observe that links pointing to useful resources (i.e., official documentation websites, tutorials, etc.) are most frequently shared, indicating the potential for tool support and the ability to provide relevant information for PM end-users.