I recently provided a method for dealing with PDFs rejected by the CM/ECF filing system (as it is implemented by the U.S. District Court for the Central District of California).  That method is detailed here.  While that process of exporting a problematic document out to a new document format (XPS) and then back into PDF deals with a number of problems, not everyone will find it to be a comfortable solution.

Here is an alternative method for removing links from a PDF, if you have Acrobat 9:

1. From the Advanced menu, select "Document Processing"
2. Choose the "Remove All Links..." option
3. Do it

That does it.  External hyperlinks distress the CM/ECF system, which, presumably, has been set to search for such links in order to prevent exploits that would lure unsuspecting clerks and judges to malicious websites.