Using either 0.12.25 or b969cdb, running the attached testcase:

vendor/phpstan analyse --level max -c testcase_require/phpstan.neon testcase_require/Module.php

An error is reported.

However, if all those files are require(d) in an App.php, and PHPStan is run on the that top level file:

vendor/phpstan analyse --level max testcase_require/App.php

...then no errors are reported.

php -f doesn't report any trouble.

I might be missing something with how PHP works, as I'm always using an autoloader.

(edited to update zip with minor code fixes - results are the same)

testcase_require.zip