Every organisation is a very complex system. It consists of soft and hard parts of a system. Their relationships and the influence of the substantial neighbourhood lead to the development of a number of problems. This article deals with nonconformities in the relationship to material aspects in management systems of organisations. Nonconformities were found from the survey which was conducted in organisations in a one region of the Czech Republic. There are from production, maintenance, store, quality department and so on. The article classifies nonconformities by a type, by a severity and by an amount. It describes the relation to risks of the management system and also to main and minor processes and to innovations. In conclusion, the article presents some recommendations for the increase of quality of a production and also for the simplification of the management system.