I've tried to reproduce the issue with just a few steps, but haven't found the exact sequence.
However, if I do the following:
1 Create a new page
2 Drag 3 application shortcuts to it.
3 Using the shortcut tiles to start and close the applications, leaving one application open.
4 Rearranging the order of the other two (closed) application shortcuts.
...then eventually (repeating steps 3 and 4) some shortcuts will begin to link to the incorrect application, and clicking on a running application will start another application instead of switching to the running application.
Needless to say this is a mayor issue for me. Inadvertently starting Visual Studio or Photoshop is really annoying and eats away at the time I hoped the application would save for me.