Youssef Hasweh expected to receive his diploma from the University of Chicago on Saturday.

What he got instead was an email from the associate dean of students informing him that, because he was under investigation for his participation in a protest encampment on the campus quad, “your degree will not be conferred until the resolution of this matter.”

Like scores of other student demonstrators across the country, Mr. Hasweh has been swept up into a kind of disciplinary limbo. Although he…