It is a problem. Short code examples can be included based on "fair use" even when the licenses conflict, but anything more substantial cannot be moved from a GPL'd file collection to a GFDL'd file collection or vice versa without all the copyright holders agreeing to a license change.
For example, you might like the example calculator program in the Bison manual; you might want to take it, enhance it a bit, and distribute it. But you can't mix it with any GPL'd code, and you might need a lawyer to help you figure out what you have to do to distribute the executable.
Copyright © 2017, Eklektix, Inc.
Comments and public postings are copyrighted by their creators.
Linux is a registered trademark of Linus Torvalds