Administrators can configure JIRA to prompt users with a confirmation before logging them out. You can adjust this setting by going to the Administration page and then clicking the 'General Configuration' link found under 'Global Settings' on the left pane.
As shown above, JIRA will never prompt users for logout confirmation by default. To change this, click on 'Edit Configuration'.
The "Never" and "Always" settings are self-explanatory. When set to "Cookie", users will only be prompted if they have logged in using a cookie (i.e. checked the box reading 'Remember my login on this computer' before they logged on).