I don't think you'll get lucky with a bug tracker supporting a file oriented bug list as such. However, most bug tracking systems allow you to file bugs related to a specific version or release number.
Giving each download a version/build/release number, and filing bugs against that number, is the way to go.
As to software recommendations, there are several questions dealing with that already:
A bug tracker that supports filing bugs against a version number and a flexible structure of projects and sub-projects is Redmine. It's my personal bug tracking recommendation next to Trac. They're both not PHP based, though.