When you go to a Michael Bay film you expect to see the same redundancy: sexy girls in revealing poses, big explosions, blue/orange filters, and glorious sunsets. But did you expect Bay to reuse the same shots from a film, he only shot six years ago?
Directors use stock footage all the time, it's a great way to save money. Now most, but not all of stock footage is parts of film that ends up on the cutting room floor. And they reuse that footage for any number of film projects down the road. If done well, stock footage will mesh like cheese and pickles. Done poorly, and stock footage will be a bigger eyesore than Leno's chin. These two scenes were not shot in 3D and had to be converted, and that is most likely the reason they caused deja vu.
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I am Jay Jayson, one of the greatest writers and researchers to ever grace the comicbookmovie.com community. If there is a story or a picture hiding on the internet I will find it.