I've had a bunch, especially with JIRA.
-Theres no way to cluster servers or have a failover machine
-Want to upgrade? Better hope your plugins will upgrade too or you'll lose data or complete issues
-Want to import a JIRA project from an older version of the app? Get set to spin up VMs.
-Want to upgrade JIRA? Take the server down and reinstall it
-Want to enable some type of logging? Take the server down and edit the shell script they start the application with (same with increasing JVM heap size).