Sorry, I can't really help here. In FireFox on a PC, the features are deleting correctly. I don't have access to an iPad or Mac to test this in iOS.
It might help to make a much simpler version of this application, which you can debug more easily. I'd create a version of this page with all the code in a single script then add a single layer and a simple add/delete function, then see if you can reproduce the problem.
That might help to pinpoint exactly where the problem is occurring - if you submit something as complex as this applicatoin to tech support, it'll be harder for them to debug.
Good luck,
Steve