* Spaces. In traditional printed text there is space between words but there are no leading spaces, double spaces or trailing spaces, so the ASCII space character is not an adequate representation.
* Paragraphs. In traditional printed text you can start a new paragraph but you can't have an empty paragraph so '\n' is not an adequate representation. Then there's the problem that some systems use '\r' or "\r\n" instead of '\n'. Then there's the problem that Emacs's "long lines" mode and Git's --word-diff don't work properly. (Almost certainly patch tools and "git rebase" don't work either.)
* Emphasis. In traditional printed text words and phrases can be printed in italics for emphasis. There are several ways this can be indicated in a computer file, but do editors and diff tools handle them nicely? I think not. Also, it's not completely clear how this should work. For example, I don't think <em></em> should be allowed, but are <em>a</em><em>b</em> and <em>ab</em> the same thing, or different things? You wouldn't be able to tell them apart in traditional printed text, but in traditional printed text you can't tell whether a space, a full stop or a dash is printed in italics, or not, either, so it's clear, I think, that we need to somewhat extend the concept of emphasis from what's available in print, but how far do you extend it? (What about nested emphasis?)