Had a bit of a strange one on a recent Exchange 2010 migration from Exchange 2003. Email sent from a Hotmail account with two PDFs but the attachments did not show in Outlook (2010 or 2013, 2003 untested). When viewing the properties of the email it reported the correct size of the total of the attachments, but no paper clip icon. If the user logged into OWA the paper clip attachment icon shows and the two attachments were present.
When the same email was sent to a user whose mailbox was still on 2003 the attachments were visible in Outlook. At this stage incoming email was still on the original Exchange 2003 server as it had not been moved to the new Exchange 2010 server. So it is clear that the two Exchange servers were handling this problematic email differently.
A quick scour of the web found this very useful post, but it was difficult to find. Here is a précis of the post: