Essay-writing is generally viewed as the primary learning activity to foster independence and analytical thinking. In this article, we show that independent research projects do not necessarily lead to critical thinking. University-level education on conducting independent projects can, in several respects, counteract enhanced analytical skills. The purpose of this study is to advance knowledge on the difficulties students experience in acquiring analytical skills. A group of undergraduate political science students were interviewed while they attended an independent research course. They were also asked to record their reflections. The digital diaries provide access to the students' perceptions regarding the assignment and their struggles as they handle scientific problems. We argue that the students are caught up in different learning dilemmas when asked to perform independent academic research. One result is that ambiguous and contradictory understandings of science affect the learning processes and thus affect the students' possibilities for developing analytical thinking.