Causality is universal relations among phenomena (states, facts, elements, functions) in the system. Verification of causality in the knowledge frame system based on principles of the topological functioning modelling can help in discovering inconsistencies such as incompleteness, ambiguity or contradictions in knowledge on system’s functioning. The method for such verification is presented in this paper. It is based on topological and functioning properties of the topological functioning model including the definition of continuous mapping between topological spaces. The method helps in discovering inconsistent combinations of cause-and-effect relations or a lack of them. Functional characteristics of the system involved in these relations are marked as doubtful. The results of verification require additional investigation by a software developer. A use of the proposed method can lead to more thorough system analysis before development of the solution.