My interpretation of the question's scenario is:
- Enter App Exposé with a four-fingered downward swipe, then
- Swipe left or right with three fingers to show the open windows from each of the other open apps (this works whether or not any windows are full-screened at the time). The windows on screen will not show the blue border highlight typical of Exposé on mouseover, and clicking on one of them will (in most cases) exit Exposé without changing focus to the clicked window.
If you reproduce this state and then perform a downward three- or four-fingered swipe, the windows will "bob" a little and the blue border highlight will reappear; clicking on the highlighted window will bring it to focus and exit Exposé, which I suppose is the expected behavior. (I believe this is what an earlier answer was alluding to.) The arrow keys will also cause the blue highlight to reappear and allow a window to be selected.
My personal opinion is that the initial lack of response to mouseovers is a bug and not intended, but I have no evidence either way. Hopefully these workarounds help, though.