I also find that if a customer uses a download manager, it often causes the link to expire prematurely because the download manager works by opening multiple connections at once, which in turn, causes the link to expire once the download manager opens up as many connections as you have set in your download limit. For example, if your links are set to expire after 3 downloads, and the customer uses a download manager that is set to open 5 connections to speed the download, then it will "use up" all 3 downloads and cause the link to expire before the download has been completed.
I find that a good solution to this problem is simply to remind your customers (preferably in the email that they are sent with the download link) to temporarily disable any download managers they might be running before starting the download.