I've encountered it once with a form, although it was a while ago and if I saw the code again I might be able to identify what was wrong. In that case it was probably a poor choice of element to attach to that caused the callback to be fired independently multiple times on one click, and stopping the bubbling had no effect.

The other time was in a Rails app, where a script was added to a partial for a layout, and then added again later on (by a different developer) to the layout itself. That caused a particularly nasty bug since it used 'toggle', and thus the second callback negated the first.