Okay I found my mistake:
In my .aspx file I had every css and js files linked with a relative path:
<link rel="stylesheet" href="../styles/core.css?v=1" />
But the deployed folder structure looked like this:
+appfolder
+++/styles
+++/Default.aspx
Solution: <link rel="stylesheet" href="styles/core.css?v=1" />
So the reference was wrong. I still wonder why (started from visual studio) the page was displayed correctly.