How frustrating that their expectations of what learning is supposed to be like sunk your project, and not something related to their actual attainment.

Did they report spending more time on it than during the traditional lecture based course? I could imagine the flipped classroom ending up making many spend more time out of class on a course, which then makes it seems like the course forces the students to do all the work.

Of course, the work of learning is always done by the student anyway, but it's less obvious when a large part is listening to a lecture.

Potential solutions that I can imagine is to put in some traditional lectures, maybe denser at the start, so that you are seen putting in effort too.

Also, making sexy posters about the "new, revolutionary, methods being used for this course" could maybe change some of the incorrect expectations about what learning is supposed to be like.