We present an analysis of the professional competencies encountered by engineering students during their capstone projects. We collected weekly reflective journals from 32 students completing their capstone projects at ETH Zurich. Through a deductive quantitative content analysis, we identified the professional competencies posing the greatest challenges for students and examined the frequency of their resolution. Additionally, we explored the distribution of challenges across different project phases and assessed their difficulty levels. Our findings reveal that while capstone projects aim to cultivate professional skills, they primarily challenge students' technical abilities. Moreover, most encountered challenges are those directly assessed through project deliverables, such as applying technical foundations that are assessed through technical artifacts and communicating effectively which is assessed through the final presentation. The majority of challenges arise during the implementation, testing, and prototyping phases, with fewer reported during problem definition and solution design phases, suggesting potential disparities in attention and time allocation across project stages. Notably, although the problem definition phase encounters fewer challenges, students perceive the challenges within this stage as more difficult. Consequently, we conclude that allocating additional time and importance to solution design and problem definition phases may effectively foster a broader range of professional skills among students, including creative thinking and decision-making abilities.