I've run across a GFX bug that seems to has something to do with text formatting and line breaks. It is a black box the size of a character, that appears in the right margin. It looks like this:

(source: it.uu.se)
On my homepage, you can view the entire document, as well as the LaTeX source. (It is on page 21.)
draftoption specified in your\documentclasscommand. This puts marks in the margin to point out places where TeX has put text outside the margins. See What does draft mode change? – Alan Munn Dec 22 '12 at 05:22GFX? – Heiko Oberdiek Dec 22 '12 at 05:38