When I use the windows client to build the jQuery Mobile App and deploy it to my iOS 9 phone there is a bug in the back button in the header.
https://github.com/Icenium/sample-jquery-mobile is the sample project link
It works fine in the simulator but on my iOS 9 device data-rel="back" is not working. This is a pretty serious bug and is a problem I am seeing with all projects we have using AppBuilder. This is the simplest one that points out the problem though.