My guess is it is down to the nesting of elements on the screen - that can get tricky, especially with very tight nesting - and that could explain why the hover over works.
Consider if you have a rectangle (A) of 20x20px, and this is nested inside another rectangle (B) of 22x22 - so there is effectively 1px of (B) around (A). If your Hotspot selection actually captured (B), if you click on this area of the screen, the chances are you'll hit (A), which isn't the one with the Hotspot assigned to it. But as you move your cursor into that area, you will pass over the 1px of (B) around the edge of (A), which will trigger the Hotspot, even though the cursor is only very briefly over (B) and quickly moves on to (A).
Press i on the keyboard during hotspot assignment and watch to see if the identified element changes as you move the cursor over/around the field. If it does, try massively increasing the zoom level to see if you can pick out the required object correctly.
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