According to Lock Haven University:
A scholarly journal is also called an academic journal. It is a
periodical written by academic experts in various subject areas. A
"peer review" journal is a subset within scholarly journals in which
the articles submitted are reviewed by researchers in the same
discipline to determine if the article merits publication. This
review process helps to ensure that only excellent and high-quality
research articles are published. All authors who publish in the
scholarly literature MUST cite sources they used in the writing of the
article, so you will find a section at the end named variously as
bibliography, sources cited, works cited, or footnotes.
A professional (sometimes called a trade) journal is a journal written
for people who work in a certain field. Grocers, resturant owners,
doctors, librarians, teachers, nurses, and other professionals need
information to help them conduct their jobs and profession more
efficiently. Trade journals are half way between scholarly journals
and magazines: they require some background knowledge but the articles
are not scholarly in nature. They address workplace issues, provide
tips on better work performance, and other work-related information.
The articles that are submitted are reviewed by professional editors.
So basically, a scholarly journal is most likely written by someone who works in academia and a professional journal is written by someone who works in industry. In your situation, you could argue that the library is at fault for mistakenly labeling the journal as "scholarly" or your professor didn't know it was a "scholarly" journal. It wouldn't hurt to bring it up to your professor and see what he/she says.