(I know we discussed this over email but I'm filing a ticket before I forget.)
See dojo/dojo@6117ba1, and https://bugs.dojotoolkit.org/ticket/15878#comment:24.
The problem happens for example when there is a <button> behind a Menu. The user clicks a menu item, which then closes the menu, and iOS sends a mousedown/mouseup/click event to the <button> rather than to the menu item.
It might also happen when tapping causes a scroll, for example opening an accordion container pane.
I don't have a test case offhand nor do I remember which platform this occurred, but I think it was iOS6. Perhaps @edurocher can help more, since it was his patch.