Well, computer science is not software engineering, and there's only so much time in a BSc program to teach one or the other.
If you were completely up front about expectations (this is about learning the processes/pitfalls of software development, not about submitting a polished assignment at the end) maybe you could give students a sense of the skills needed to succeed not just at computer science, but software dev as well.
Sounds like CS320 at UMass Amherst. We all considered it one of the most work-intensive courses in the degree.