Objectives Errors in clinical reasoning are a major factor for delayed or flawed diagnoses and put patient safety at risk. The diagnostic process is highly dependent on dynamic team factors, local hospital organization structure and culture, and cognitive factors. In everyday decision-making, physicians engage that challenge partly by relying on heuristics – subconscious mental short-cuts that are based on intuition and experience. Without structural corrective mechanisms, clinical judgement under time pressure creates space for harms resulting from systems and cognitive errors. Based on a case-example, we outline different pitfalls and provide strategies aimed at reducing diagnostic errors in health care. Case presentation A 67-year-old male patient was referred to the neurology department by his primary-care physician with the diagnosis of exacerbation of known myasthenia gravis. He reported shortness of breath and generalized weakness, but no other symptoms. Diagnosis of respiratory distress due to a myasthenic crisis was made and immunosuppressive therapy and pyridostigmine were given and plasmapheresis was performed without clinical improvement. Two weeks into the hospital stay, the patient’s dyspnea worsened. A CT scan revealed extensive segmental and subsegmental pulmonary emboli. Conclusions Faulty data gathering and flawed data synthesis are major drivers of diagnostic errors. While there is limited evidence for individual debiasing strategies, improving team factors and structural conditions can have substantial impact on the extent of diagnostic errors. Healthcare organizations should provide the structural supports to address errors and promote a constructive culture of patient safety.