That sure is strange and should of course not be the case (and it is not for me). For this reason I would like to ask:
Which version of yEd are you using (see "Help" -> "About")?
On which operating system are you using yEd?
Please upload a GraphML file with your diagram before applying the hierachic swimlane layout (see How to upload files to yEd Q&A? for instructions on uploading files). Otherwise it is almost impossible for us to reproduce and understand your problem. Since this is a public forum, please make sure nothing you upload contains sensitive information.
Please upload the file "settings.xml" from your yEd profile directory (see "Help" -> "About" for the profile directory location) as well.
Here is my graph before applying the hierachic swimlane layout
Well, running the hierarchic swimlane algorithm with default settings except for orientation left to right on your diagram works as intended for me (yEd 18.104.22.168, Java 1.8.0_181, Ubuntu 16.04).
Maybe you are using a specific combination of settings that triggers an incorrect behavior. Thus we really, really need your settings.xml file as well. Moreover, if you could also upload a version of your diagram after you have run the hierarchic swimlane algorithm that would help as well.