I've already filed a bug report about this, so this post is just providing the quick work around people can do so that this issue doesn't hold up their projects.
You may or may not have discovered yet, that exported Mac apps ignore the hotspot location of active objects while doing a transition. So if your hotspots are typically at the centre of an object, you'll see it way out of alignment until the transition is done.
To get around this, for the time being, make all of your hotspots 0,0 since that's what they become during transitions. This way, what you see in your preview will match up with the results of your Mac app.