You have a point. It might be just showing contamination. But with circumstance like air bubbles and water sound just started right after that zooming, it is obvious in water. ah… I don't know. I think this might show transition to something else, as I have already said. Just confirm my opinion.
Anyway, zooming in dark spot is too vague to interpret transition to witch's barrier = = And falling into white window is much more better on that.
There were so many windows show up… like randomly. There are also 'non-white' window or window with 'colorful squares and circle around them' .For example, outside Kyubey's isolation field with dark window, colorful window that show the past, and on Blu-ray Box (We can see Madokami and Homura with her dark wing inside. Madoka didn't show in Madokami from inside barrier for sure. But if we take out stuff in the box, we see Nightmare barrier! this window represent Homura's barrier! Too much vague thing here = = )
Anyway, white windows were most relate to Madoka or boundary and other type of window seem to relate to boundary? past? or just random Inu Curry things? I don't know. However, are there anyone can tell about "Window tower" in the way to Kazamino? Ton of dark windows. Do we have something to do with this tower? Anyone know weather it interpreted something?
Lastly… In the end of my (crazy long) reply, soul gem falling scene(again = = ) there was Madoka's voice. I wonder what she said??? or just randomly dialog from some movie?