Quite a few people have reported issues with objects not aligning correctly in cutscenes; cell phones hovering a foot away from a hand, npcs with half their body stuck in chairs, and the most common screenshot of all, Tobias with his flight helmet bisecting his head with the greatest subtitle ever.
It looks like iZfaN, Jacknief, and Jon may have just figured out the cause and have a potential solution. From testing and other user input, they came to the conclusion that higher framerates past 30 are what actually causes the bug, and simply limiting the framerate to 30 with an app like DxTory will make everything line up correctly. More input is needed, so please try it out and let us know in the comments!
If this does end up working for everyone, Powertools currently monitors for cutscenes, so we may be able to integrate a fix there for a more elegant solution.
Additional info about the bug in our thread that Volition is looking at can be found here.