The problem WYSIWYS is trying to prevent is that, when the same file is displayed with different software, or at a different time, or on a different system, etc, it may be displayed differently, even though the binary data is the same.
Imagine someone crafting a web page that displays differently in different browsers. If someone downloaded it as an HTML file and signed it, they would likely assume they had signed exactly the content they saw when they downloaded it, but another user who opens the HTML file in a different browser will see something completely different.
Another example is a document with external references (think images in a web page), even though the user is shown the image before signing the document, what they're really signing is a reference to that image. The user thinks they signed a document that includes the image, but the image being referenced could be modified without invalidating the signature.