Emulator in XDK is just another web browser, not device emulator. It emulating device resolution and some other functions, but this is not real emulator, like a in Eclipse or other real SDK's. However, XDK is very good tool, don't get me wrong.
With your problem, you can disable click "possiblity" for some time, maybe 1s after click, then turn on it again. And good habit is do not place buttons on different layouts in same place (real place on device), because after clicking "go layout 2" you can click also on layout 2 back button for example if is in same place. You must be tricky a little.
If you have no real device, is much harder. You should have it, but I published my 1st game without and here was no problems, but a lot of pain with checking how it should work.
If you are working in XDK and you are using sounds, you should use Crosswalk only, because here sound will work 99% where other exports, without some magic, it will not work on 99%.