While debugging an issue with isort's behavior in sorting imports, the author encountered a misclassification of a custom module as a third-party one. The problem arose when using isort with pre-commit, which sorted the imports incorrectly due to the default configuration setting that classified the custom module as "THIRDPARTY." The author used various debugging techniques, including running isort independently with specific flags, inspecting the isort source code, and examining configuration settings, to identify the root cause as an import path issue. By adjusting the isort configuration to recognize certain directories as local with the "known_local_folder" setting, the author resolved the issue and ensured proper import sorting. This experience highlighted the importance of creating reproducible test cases, utilizing verbose output for insights, and leveraging source code inspection to understand and resolve configuration-related issues effectively.