Steps to replicate

1. Configure JIRA to use CROWD user directory and then synchronize
2. Enable the alias feature in Crowd and add an alias to a user
3. In JIRA, synchronise Crowd directory again
4. Login to JIRA with the username (not the alias user)

When viewing the list of users in JIRA, it will display both the username and the alias, thus create two accounts for a single user

Workaround:

Re-create the Crowd Directory again. For example, remove the Crowd directory in JIRA and then re-configure the Crowd User Directory. Lastly, synchronise JIRA with the Crowd directory.