If I enable the auto-rotate with edge property on an arrow it rotates the label in the wrong way (it apparently seems flipped around the y axes): file with this bug
I cannot reproduce this problem in the current version of yEd (which is 3.19 at the time of this writing).
Can you share a GraphML file that demonstrates the incorrect rotation? Please see How to upload files to yEd Q&A? for information on how to upload files here.