Its called black clipping, a sudden color drop to black instead of a smooth transition. This not only happens to movies but everywhere including images,games and the UI.
It is caused by an incorrect gamma profile loaded up on the Galaxy Note and Galaxy Nexus and so far Samsung didnt comment about this issue considering a lot of people already have the Galaxy Nexus.
On some screens this clipping appears differently, this is a huge deal breaker for me gyud as I watch a lot of movies on my phone.
Anyone with a Galaxy Note can test this video clip from Iron man 2:
IM2_Sample3.mkv
Use the stock player with brightness set to 0
Watch in a completely dark room to avoid reflections
Set the screen mode to 'standard' ( settings > display > screen mode )
Those apps will auto rerun anyway once closed, dli kaayo advisable mang task manager ka to auto kill apps as it would drain a lot of battery.
Removing unwanted stock applications is the better solution, root your phone and download titanium backup.