Background: Hyper-video technology allows reflection on learning materials by writing personal notes and by interactions with lecturers and peers through shared posts and replies. While research shows that integrating hyper-videos in educational systems can promote the learning processes and outcomes, an open question remains regarding its actual utilization patterns by students and teachers. Objectives: The study aimed to reveal the extent to which students utilize different functions of hyper-videos in real-life learning contexts, and to examine the role of instructional design on hyper-video utilization. Method: In a mixed-method design, the study characterized active and passive interactions in hyper-videos in higher education courses, and amongst active interactions, compared shared versus private annotations. Additionally, the study compared voluntary and mandatory instructional design for promoting hyper-video interactions. In particular, we used learning analytics to explore hyper-video patterns in 25 undergraduate and graduate courses. Results and Discussion: A log analysis revealed that students wrote most of the posts, while lecturers mainly provided replies to students' posts. Private annotations were more prevalent than shared writing, pointing to the unfulfilled potential of hyper-video annotations to benefit from collaborative learning. A qualitative analysis on instructional design was consistent with quantitative findings, revealing important differences between the courses with mandatory versus voluntary hyper-video integration in pedagogical design, and in cognitive presence and teaching presence, based on the community of inquiry framework. Major takeaways: Findings point to an unfulfilled potential of hyper-video technology to promote active and collaborative learning. This highlights the role of design and instructive guidance when integrating technology into educational systems.