The new LibreOffice supports exporting PDFs in a hybrid ODF / PDF file format. When trying to upload such a file MediaWiki reports that the ZIP file is ambiguous or has been damaged. (I have a German installation so I can't tell you the exact error message.)
I already took ZIP files out of the MediaWiki Blacklist and added the file extensions PDF, ODT and ZIP.
I think includes/ZIPDirectoryReader.php checks the file and throws out the error cause it doesn't know the new file format yet.
The new PDF / ODF hybrid format makes it easy to open documents for everyone while maintaining the possibility to edit them which might also be a great thing for Wikipedia. Therefore, this is a major bug for me.
Please fix this and thanks for the great software.