Because in this particular case, the producers (game developers) are actually pretty much OK with people using their "content" in Youtube videos, and indeed, probably benefit from it.
Unfortunately the Youtube system is structured mainly to handle the opposite case, where the producers are insane jealous spawns of evil who will scream shrilly at the top of their lungs at even the merest hint of faint resemblance (if you look with your eyes blurred while drunk) between a video and their "content."
So basically Youtube's automatic system is being over-eager in tagging a bunch of stuff as potential copyright violations, when it's probably OK to not do so for much of it....
As somebody else said, there's likely a technical solution to this by improving the ability to whitelist content from consenting producers.
