I was copying text (including e.g. bullet points) from a pdf file into the data->Description field of a node. Although these special characters looked funny, yEd had no problems with this. After saving and quiting yEd I tried to re-open the file, but then an error occured with an obscure java/xml/sax(?) explanation.
Since I suspected the copied text from the pdf file, I edited the graphml file to remove the special characters. Then I could reopen the file in yEd.
It is an error that I can insert characters in a text field in yEd that makes the graphml file unreadable for yEd.