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Originally Posted by Ilidsor
Because the manga is written by the author of the Index LNs. That would be like considering the Percy Jackson movie canon over the books. The anime messed up making some of it's events not canon, not making some of the manga's events not canon.
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Although one can consider the anime with it's differences as a different version / slight AU of the universe, and in that case you can consider it to be it's own canon.
But the problem with doing it for Index/Railgun is that while the animes have some differences with source and some original content they're still following the source instead of going full original and/or making an original end.
This does mean that anything they add/cut/change can result in later having to add/cut/change more things to fit future arcs without contradict what the anime showed before.