Path in Payload is missing from Bom

I'm trying to submit an App to the App Store and keep getting an error which says the following:

This bundle is invalid - Package "swiss.mandelkind.iBookmarks":
Path "iBookmarks.app/Contents/Resources/Python/site-packages/Crypto/Signature/.___init__.pyo"
in Payload is missing from Bom.

This is due to a dependency I have to put into the bundle and I simply copy this with a cp -RP command using a Run Script Build Phase.

I made sure there is no such hidden file before and after copying.

That said, if I have a look at the created app archive, everything looks good, that is the .__init__.pyo does NOT exist.

But as soon as I export the app for app store and trying to submit it, the above error is thrown.

Any idea how to fix this? The only similar thing I was able to found in the net is the following - unfortunately without any hint or solution:

"ITMS-90000" :This bundle is invalid. Package "org.xpra.pkg": Path "Applications/Xpra?.app/Contents/Resources/lib/python2.7/numpy/f2py/tests/src/assumed_shape/.f2py_f2cmap" in Payload is missing from Bom.

Worth mentioning: I'm trying to upload the *.pkg using Application Loader.