We have some wonderful users who, when faced with a file upload that only accepts .PDF, will happily rename their .TXT, .PNG, or whatever and attach that. The file upload doesn't seem to care, but the Save to Repository task will fail with the exception, "PDF header signature not found."
My best guess to handle this so far is to add a workflow immediately after the form submission that uses Retrieve Business Process Variables, For Each File, and a C# Script to check the header of the file for the identifying "%PDF-". I'm not sure, though, how the script can interact with the files--are they in the file system somewhere that the workflow user will have access to?