I would choose the one the majority of the object is over. I understand your point, but I think that when the learner clearly selected the incorrect option, the result should reflect that choice.
Storyline knows which object that is as well. If I change the Drag Item Options to return if dropped outside "any drop target" instead of "a correct drop target", and drag the circle as shown in my screenshot above, it snaps to the intended box, Drop Target 3.
And it doesn't appear to have anything to do with stack order either. If I do the reverse, dragging Drag 1 over Drop Target 4 and just touching Drop Target 3, it will snap to Drop Target 4 if "any drop target" is selected.
The behavior seems to me to be inconsistent. It also makes developing interactions where the drop targets are necessarily close, like using pieces of a pie chart as targets, more difficult.
Thankfully my client was ok with me redesigning the interactions to spread the targets out so that overlapping two at once was impossible. But it would be great if this behavior with "a correct drop target" was optional.