The only true way to know what the file versions are is to check the "Details" tab in the file's properties page to see if both the extracted and the one in the installation are the same or not.
The best way to avoid this is to create a restore point or system image before modifying any system files. This way you could easily use it to restore the file if something bad happens to it.
If you look up the KB number of the hotfix in the search box at the top of Microsoft Support
, it will give you a complete list of files that it will effect. For example, KB2448827 for a IE9 update