Your refusal letter is a template. The officer ticks one or two boxes such as “purpose of visit” or “ties to home country”, and the same letter goes to thousands of people. It does not say what in your file caused the tick.
GCMS is the Global Case Management System, IRCC's internal database. CAIPS was its predecessor and the name has stuck. When an officer reviews your file they write working notes into it: which documents they looked at, what concerned them, what they checked, and the reasoning behind the decision. Those notes are the reason. They can also contain things you never saw, such as a note that a document looked altered, a mismatch between two forms, or a flag carried over from an earlier application.
The notes package normally runs 10 to 40 pages. It includes the officer's comments, the eligibility and admissibility assessments, a log of every action on the file, and, if you order the file as well, copies of what IRCC holds. See a real redacted example.