Automation is an important feature in-flight operations and its implementation in aviation has brought numerous benefits, such as reducing the workload and optimizing operations. However, there are difficulties in crew interaction with automation, such as autopilot mode confusion. To expose which mode confusions are usually prevalent and recurrent with Brazilian pilots, a survey-style questionnaire was administered to airline pilots. The survey results, answered by 145 pilots, reveal that the average frequency of mode confusion is 2.01 ± 0.40 occurrences per year and less experienced pilots are more likely to experience the phenomenon. This research points out that the prevalence of the phenomenon of mode confusion occurs in the final stages of flight, the vertical navigation (VNAV) modes being the most complex and confusing to pilots. The research also presents the main causes of mode confusion, as perceived by the pilots, their consequences, and mitigating measures. Data collected in this study can be used in future studies and by airlines to develop mitigating actions to manage the risk of mode confusion.