Well localized the problem (without understanding it so far)
It was not the .htaccess file.
It was not plugins or themes (which I deactivated all to see what happens)
But my little php app had their own session handling and modified the header. Just simple textbook stuff (login etc..) which works flawless outside WP.
I didn’t analyse why this happens, but without the session/header stuff my php app works fine alongside WP.
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