Hi there, if you're only wanting to remove document access/sharing for one specific project, it should work when you remove their access to each document in the issue/project - you are breaking the inherited permissions that way (be sure you're removing their access on documents but they'd still have access on the project).
If you're wanting to do this more globally, and this set of users is a lower license level, remember you can do this through access levels. In Setup > Access Levels, go to the license in question and select the checkbox towards the bottom about not automatically inheriting permissions. We use this for our Reviewer licenses - just note that when you DO want them to see docs, that means they need to be shared with those users for any document you intend for them to see (a habit some of our org has not gotten in).
If this helped you, please mark correct to help others : )