The visibility of issues can only be restricted by assignigt an issue security scheme to the project and then selecting an individual security level for an issue while you edit it. But in the edit form this field is called 'security level' and you can select the level from a select list which contains all the security levels contained in the security scheme.
From what you write i assume you selected the permission on the comment that was entered while you edited the issue. This comment level security just applies to the comment, not the issue. That's why the visibility on the issue does not change. You just affeçted the visibility on the comment
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