When performing an audit in License Manager, users are listed under licenses that they are currently using. These privileges can be inherited from security roles, can be assigned directly to the user, or can be inherited from any group to which the user belongs including the "everyone" group. This document demonstrates how to determine the source of such privileges:

To see which privilege is causing a user to hit a particular license, expand the user name. The privileges listed are the ones associated with that user:

Opening this user in Strategy Developer through User Manager, select the project access tab and locate the license area for the licenses listed in License Manager:

Privileges that are inherited from either a group or security role cannot be de-selected at the user level. Such privileges must be de-selected from the group or security role from which the user is inheriting it.
The color of the check mark indicates whether the privilege is being inherited from the user/group level or from a security role. Blue indicates it is being inherited from either the user level or the group level. Green indicates the privilege is assigned to a security role which is assigned to the user. A key to these colored check marks is located at the bottom of the user manager window:

In the above example, notice that four of the privileges are inherited from User/Group level and one is from a security role.
Expand the first column to obtain additional information about the source of the privileges:

In this example, the source of the privileges can now be discerned:

If the user should not have that security role, click on the name of the security role and select "+Inherited Access," as below:

After removing the security role and editing the user privileges and the privileges inherited by the group, the user appears as follows:

Checking the license audit reveals that this user is no longer using a license for Developer Analyst:

Note: Restarting the Strategy Intelligence Server may be necessary to ensure that License Manager is displaying changes to user privileges.