png's created (exported) with yEd have "undefined" as value for the "Units" parameter. This causes incorrect sizing in LaTeX (Units: Undefined).
See this post: http://tex.stackexchange.com/a/10399/70241 for more information.
Well, the meta data you mention is optional in PNG images. If LaTeX cannot handle PNG files without meta data, this is a LaTeX shortcoming, not a yEd problem.