If you have a big project, you can add folders in "documents" and change visibility for each group. So not all Team members can see all documents.
So for documents is possible to split the project in several subprojects.
In "issues" you don't have this possibility. Everyone can see all issues, no subfolders are possible. The only wordaround is to make an own project for each subproject of the overall project. But then some other features like timeplan and and and must be coordinated extra. It would be very nice, to make folders also in "issues".