Jira delegated usermanagement to crowd.
JIRA license limit depend on the group assigned to the user. Although Crowd server has deactivated the user from login to JIRA, JIRA does not know that the users has been deactivated and still count the user to the license limit because of the group assigned to the users.
This is just a limitation between JIRA and Crowd.
Jira should be aware of crowd's inactive flag and should not count deactivated users against its license limit.