By default, all employees see all projects. You must be using either project assignments (Projects > General > Assignment) or Manage Access (Settings > Access & Permissions) wherein restrictions come into play and employees get to access only assigned projects and items. When you don’t assign any employee to any project, all employees have access to projects. So, you should assign employees to only those projects that you want to hide from others.
If you have enabled Manage Access, employees have to be added to projects. This is what is happening in your case. We recommend turning Manage Access off and using project assignments instead. Check CORE Help Center for details.