Internships in science research settings have received increasing attention as a means of helping students construct appropriate understandings, practices, tools, and language in scientific activities. To advance student-scientist partnerships beyond the status quo, the study aimed to investigate how cogenerative dialogs (cogens) may help high school students and scientists identify and address challenges collectively. The analysis identified nine major challenges discussed during cogens: (1) the quality and progress of scientific practice in laboratories, (2) the quality of scientists'/assistants' instructions in classrooms, (3) the quality of student participation in classrooms and homework, (4) students' absences, including arriving late or leaving early, (5) the quality of administrative support, (6) preparation for scientific presentations, (7) the process of deciding project topics, (8) students' peer interactions and communication, and (9) students' physiological needs. The three most salient challenges were "the quality and progress of scientific practice in laboratories" (39%), "the quality of scientists'/assistants' instructions in classrooms" (20%), and "the quality of student participation in classrooms and homework" (17%). The study shows that cogens allowed students and scientists to agree on teaching modifications that positively influenced teaching and learning processes during the internship, such that issues were reduced from the beginning to the closing stages. Importantly, the challenges and solutions identified by students and scientists in this study provide accounts of first-hand experience as well as insights to aid program directors or coordinators in designing a learning environment that can foster effective practice for internships by avoiding the issues identified in the study.