When configuring Crowd to use Active Directory as its main directory, you will have to set a user filter so as to fetch only the users that you want to be seen by Crowd. So you might have thousands of users in AD but you can decide to get only 100 of them in Crowd and thus rely on a 100 users only license.
Please take a look at the following page for more details: https://confluence.atlassian.com/display/CROWD/Restricting+LDAP+Scope+for+User+and+Group+Search
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