Several moments displayed by Venom Snake in Mission 43 are prominent in the trailers, but aren't in the game proper (apparently, most of these were edited by Hideo Kojima to play up certain themes present in the plot, and were never intended to be in the game itself). Among these is a shot of Venom Snake staring away from the flames while cremating his infected troops in Mission 43 (while his face is covered in blood) and a transitional shot of Snake's face turning into a skull (which provides the page image for the game's associated Nightmare Fuel page).
A cutscene of Venom Snake walking through a burned African village, dropping to his knees and screaming up at the sky doesn't appear in the final product, although most believe that these animations were repurposed from Mission 43 ("Shining Lights, Even in Death") where Venom does the exact same thing after he's forced to kill his infected staff members. In the final game, there is a burned village (north of Masa Village) that can be visited and a short cutscene that plays with Miller explaining what happened when you approach a pile of charred bodies, but not the exact sequence seen in the trailer.
Another trailer showed footage of a prisoner (dressed similarly to those encountered in Ground Zeroes) being tortured before being shot in the back, in a location that looks very similar to Camp Omega from the same title. While there were claims that this was part of an unrealized Old Save Bonus that would have been accessed through a data transfer and would have involved the player going back to the same location, this cutscene never appears in the game. However, the animations seen in this footage are accessible during Mission 6 ("Where Do The Bees Sleep") if you follow the soldiers transporting the Hamid prisoner into Smasei Fort all the way down to the basement and not trigger any combat alerts, you can see the soldiers find the Killer Bee and taunt the prisoner before executing him in the same way as the cutscene.
Several trailers showed footage from a cutscene in Africa of child soldiers being trained to fire assault rifles by an instructor. While the kids training with the instructor can be seen in the final product by going to Masa Village during Mission 13 ("Pitch Black"), waiting until dawn then watching the kids training with the instructor, this doesn't appear as a cutscene.
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