In this paper some of cognitive contradictions and complexities of system thinking have been discussed. Organization theory helps changing managers' thoughts, developing their conceptual models and improving their performance. Indeed the effectiveness of system management is found when system's knowledge cognition takes place in an interaction of conceptualization and a concept taking free from contradictions and non-alignments. By pondering on management principles, we concluded that there is a clear and in some cases intangible relationship between them and the system features. So, by digging deep into this theory, some of the vague and conflicting issues were identified. Moreover, in recognizing the problems of systems including organizations and humans, in addition to the ambiguities that each of them are mentioned as one of basic methods for solving systemic problems, there are obstacles against discerning and employing systemic thinking in our society. Finally, to deal with these confusions and obstacles, some effective guidelines and instructions have been proposed.
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