phpstan/phpstan is not scoped through the scoper project and it is declared as a dependency of the rector/rector package. But the phpstan/phpstan package is still committed in https://github.com/rectorphp/rector/tree/9a8a2a24dd650317b66950330cb77072949d9454/vendor/phpstan

For IDEs that index the content of phars present in the vendor folder (which is good when using phpstan as it allows to know about its classes), this cause the IDE to detect duplicate class definitions for phpstan classes, as we have 2 phpstan phars in the vendor folder (the one coming from installing phpstan and the one bundled in rector).