What's the difference between the components ending in .system and .module in the Bug tracking system?
You're reading things slightly wrong.

There's no file.system component, or any other component ending with .system.

There are systems:


ajax system
batch system
file system
etc...


These are for issues pertaining to parts of Drupal that are not located in a module. Anything in the /includes folder of a normal Drupal installation, basically. (ajax.inc, batch.inc, file.inc for the examples above)

Then there are modules:


blog.module
file.module
menu.module
etc...


These are for module-specific issues.