Encouraging students to participate in collaborative discourse allows students to constructively engage one another, share ideas, develop joint understanding of the course content, and practice making scientific arguments. Argumentation is an important skill for students to learn, but students need to be given the opportunity in class to engage in argumentation. To investigate the importance of instructor facilitation on argumentation, two iterations of one instructor's Process Oriented Guided Inquiry Learning (POGIL) physical chemistry course were studied using the Toulmin analysis and the inquiry-oriented discursive moves frameworks. Data were collected by recording class conversations and interactions taking place in the POGIL classrooms. Initial analysis of an individual instructor's implementation of the POGIL materials provided data regarding the nature of small group and whole class interactions and the nature and quality of student-generated arguments. The instructor was then able to make modifications to the facilitation of that course for the next iteration of the course. Data were collected for this subsequent implementation, and the two sets of implementations were compared. It was found that slight changes in facilitation can lead to significant differences in the types of student interactions and the nature of students' arguments. Simultaneous reporting was useful in encouraging iterative argumentation and discussion among students, and setting expectations that students must be ready to explain how they solved the problem and justify their work helped students develop their argumentation skills.