After changing the font of my nodes from the default "Dialog" to "DejaVu Sans", the resulting PDF file would render the node labels upside down, i.e. reflected along a horizontal line, presumably the base line of the text. This only happened when embedding the font into the PDF, not when converting the texts to outlines or when relying on the font being installed on the target system.
This was observed using yEd 3.10 on Gentoo Linux.