We can assure you, the files are different.

So you opened up the file in a text editor... then you got the original WordPress.org file and opened it up too... and they appear to be completely identical, right?

This means our scanner is broken?  No.

One of the common problems here is "new line characters" and the differences between Windows, Linux, and Mac.  If you don't know what we're referring to, that's okay, trust me when I say they are different, even though you can't actually see the difference.

If I can't see any difference, why does the scanner report the difference?

Because the scanner is smarter than all of us put together.  The scanner's job is to find differences, not to discern whether they're important or not. Whether it's important is our job as WordPress administrators.

The most likely cause of this problem is that the WordPress.org files used in your particular WordPress.org installation were sourced not from WordPress.org.

Instead, a 3rd party installer tool was used which, somewhere along the way, converted the new line characters to that for the native platform. Or perhaps you downloaded a ZIP and the files in there have different line endings in them.

Why is it like this? We may never know, but it happened.  So while the file is OK and there's nothing to worry about, it's still different.

This is where your role as a WordPress administrator comes in - you need to make the executive decision - repairing/replacing core WordPress files.