Does this happen when you try to import the GEDCOM file or do you already have a diagram in yEd that you are trying to arrange with "Layout" -> "Family Tree"? If the former, can you upload your GEDCOM file here and post screenshots of your import settings? If the latter, you can you upload a GraphML file of your diagram here and post screenshots of your family tree algrotihm settings? Please see How to upload files to yEd Q&A? for instructions on uploading files.
Which version of yEd are you using?
On what operating system are you using yEd?