This is very strange, but after rebooting Xcode and clearing the build folder (only one command + alt + shift + K in response to the @Matthias comment) the warnings disappeared.
I say weird because I saw them for about a week (after I extracted a couple of small C function functions like Cocoa Pod and started importing them into my .pch file).
I will provide more details here if I ever see this behavior again and notice any details on how this can happen.
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