Files are distributed as part of a larger project. A file with individual build version x might be distributed as part of project version y.
To elaborate: A.exe with product version 1.1 ships with files B.dll and C.dll. All start out with matching product and file versions. Then someone finds a serious bug in the product. The developer looks at it, and issues a fix that only updates B.dll. Now the product version probably updates as well, to 1.1.1 to account for the minor fix. And B.dll’s file version will also be 1.1.1. But A.exe and C.dll didn’t change, and so their file version might still be 1.1.