When I try to download a PDF using Safari, it will save to my Desktop, but when I go to open it, I get the error "There was an error opening this document. The file is damaged and cannot be repaired." If I try to use the Print command and save it as a PDF, I get nothing but a blank document.
The following article from TUAW may be of help: http://tinyurl.com/9tqn45d. It states that the problem may be caused by 'AdobePDFViewerNPAPI.plugin' in the Internet Plugins folder. Deleting that plugin seems to fix the problem for many people.
I don't have this problem even though I have the 'AdobePDFViewerNPAPI.plugin' installed. Perhaps the reason I don't get the error message is because I use the Adobe PDF Viewer as my default plugin for viewing PDFs in Safari. In fact, if I remove the 'AdobePDFViewerNPAPI.plugin', I can no longer see PDFs in Safari, only download them.
So, the error messages may exist only for users of Safari's built-in PDF-viewer. I find the Adobe Plugin has a few more tools than the built-in one. Using that one may be an alternate solution to this problem.