MODX ACTION_UPGRADE copies the new package tree and does not delete files that left the Extra. Leftover processors under core/components/minishop3/src/Processors/ remain callable via assets/components/minishop3/connector.php.
When you delete a PHP file from the shipped component (core/components/minishop3/ or assets/components/minishop3/), add its path to:
core/components/minishop3/config/obsolete_package_files.php
Paths are relative to that component root. Missing files on a site are skipped (not an error). The upgrade resolver _build/resolvers/resolver_10_obsolete_files.php purges the list via MiniShop3\Utils\ObsoletePackageFiles with path confinement under the component directory.