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This study establishes the first empirical taxonomy for runtime faults in Model Context Protocol (MCP) servers, a critical infrastructure layer enabling Large Language Models to interact with external tools. By analyzing 833 fault threads across nearly 500 repositories, the research identifies 73 specific failure types ranging from schema enforcement issues to security validation gaps, validating these findings through surveys of active developers. The resulting framework provides essential diagnostic clarity for maintaining reliability in rapidly evolving tool-augmented AI workflows.
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A Taxonomy of Runtime Faults in Model Context Protocol Servers

arXiv2 min read

arXiv:2606.05339v2 Announce Type: replace-cross Abstract: MCP (Model Context Protocol) enables LLMs (Large Language Models) to interact with external tools and data sources via a standardized protocol. Its rapid adoption in tool-augmented Artificial Intelligence (AI) workflows has introduced new reliability challenges, such as configuration parameters that are accepted but not enforced at runtime, leading to unintended default behavior, whose runtime fault characteristics remain empirically unexamined. We present the first empirical taxonomy of runtime faults in MCP servers. We manually analyzed 833 confirmed runtime fault threads identified through a repository-mining pipeline covering 473 actively maintained MCP server GitHub repositories and derived a taxonomy using a bottom-up open coding procedure. The taxonomy comprises 11 top-level categories and 27 subcategories (73 leaf fault types), covering recurrent failures across protocol interactions, tool invocations, schema enforcement, state management, model-provider integration, security validation, and timeouts or explicit cancellations of in-progress operations. To assess the taxonomy's external validity, we surveyed 55 MCP server developers. Respondents reported experiencing an average of 20 of the 27 fault subcategories, and no category remained unobserved. These results indicate that the taxonomy reflects widely observed runtime failures in MCP-based systems and shall assist AI software maintenance and evolution in the future.

Abstract:MCP (Model Context Protocol) enables LLMs (Large Language Models) to interact with external tools and data sources via a standardized protocol. Its rapid adoption in tool-augmented Artificial Intelligence (AI) workflows has introduced new reliability challenges, such as configuration parameters that are accepted but not enforced at runtime, leading to unintended default behavior, whose runtime fault characteristics remain empirically unexamined. We present the first empirical taxonomy of runtime faults in MCP servers. We manually analyzed 833 confirmed runtime fault threads identified through a repository-mining pipeline covering 473 actively maintained MCP server GitHub repositories and derived a taxonomy using a bottom-up open coding procedure. The taxonomy comprises 11 top-level categories and 27 subcategories (73 leaf fault types), covering recurrent failures across protocol interactions, tool invocations, schema enforcement, state management, model-provider integration, security validation, and timeouts or explicit cancellations of in-progress operations. To assess the taxonomy's external validity, we surveyed 55 MCP server developers. Respondents reported experiencing an average of 20 of the 27 fault subcategories, and no category remained unobserved. These results indicate that the taxonomy reflects widely observed runtime failures in MCP-based systems and shall assist AI software maintenance and evolution in the future.

Software Engineering (cs.SE); Artificial Intelligence (cs.AI)

arXiv:2606.05339 [cs.SE]

(or arXiv:2606.05339v2 [cs.SE] for this version)

https://doi.org/10.48550/arXiv.2606.05339 Focus to learn more arXiv-issued DOI via DataCite

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Full text under the publisher's open licence · 288 words

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