Knowledge based systems’ design requires the developer’s advanced analytical skills. The efficient development of those skills within university courses needs a deep understanding of main pitfalls and drawbacks, which students make during their analytical work in form of visual modeling. Thus, it was necessary to hold an analysis of 5-th year students’ learning exercises within courses of “Intelligent systems” and “Knowledge engineering” in Saint-Petersburg Polytechnic University. The analysis shows that both lack of system thinking skills and methodological mistakes in course design cause the errors that are discussed in the paper.