why was thomas feeling responsible for everything that was happening?

Thomas feels responsible because of his discoveries and his sense of rebellion. Thomas's discovery of the graveyard, and the morbid grave site of the young boy who tried to escape via the Box tunnel, only serve to further cast the environment as one in which life is constantly vulnerable. Awaiting the Gladers outside the protective walls is a world run by monsters where they would likely die violent deaths. The fear of painful and unpleasant deaths, rather than the fear of simply being dead, serves to control the children and limit the chances they are willing to take.