It sounds like you are trying to transfer the files from a Windows machine to a Linux machine. Have you tried extracting directly from the tar file onto the server?
There are several symbolic links related to the Datacite / Crossref classes, and Windows and Linux handle them very differently. Git on Windows is also spotty with symlinks. If you’ve extracted the files on a Windows machine and then try to upload them via FTP/sFTP or zip them and move them to a Linux machine for unzipping, these symbolic links will likely be broken.