Without the appropriate facilitation of discussion in a problem-based learning (PBL) course and the use of specific educational tools that enhance cognitive skills, students might deprive themselves of achieving the deep learning experience expected to take place in a PBL course. One of the educational tasks in PBL is the creation of mechanisms for hypotheses made by the students, based on their knowledge of the basic sciences and the psychosocial issues raised in a particular case scenario. The whole task is student-constructed and should enhance their ability to explain the scientific basis of the symptoms and clinical signs of the patient enlisted in the case. Because students usually discuss the case without enough prior related knowledge, they might find it difficult to address different aspects of their mechanisms. These gaps in knowledge may be considered part of their "learning issues". In tutorial 2 (a PBL case is usually discussed in 2 or 3 tutorials at the maximum; each tutorial is 2 hours long), students should be able to build a comprehensive mechanism reflecting their deep understanding of the problem. However, students might not be able to integrate information learnt and their mechanisms might show a number of shortcuts and/or lack integration of information, and the flow of the pathophysiological changes may not be logical. This manuscript describes 5 key open-ended questions in PBL tutorials to facilitate students' discussions as they create their mechanisms.