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The X manga had certain aspects of it that, well, people didn't like, people who specifically are in the government, or/and who run/ran the publishing company that the series was once serialized in.

Also of course anytime a manga/anime has aspects of decapitation or dismemberment as soon as something like that happens in real life, the first to be blamed are manga/anime etc. It's also an easy excuse for those that does these crimes to say they got the idea from 'said' manga/anime. USA has had many incidents like these, thou often involving firearms, and the blame being on movie and video games.