Catalina is part of Apache Tomcat, which is a web services environment. That tool is not part of the default contents of the Dock on OS X Server 10.6, so it's been added. If you don't want it in the Dock.app, then drag it off the Dock.app. Might also want to see if Tomcat is being automatically launched during bootstrap, if you don't want that. Usual launch would be via launchd or maybe via a login item or via a web-related start-up.
Which implies there's something else going on here, or something else that's concerning you related to the OS X Server environment. Could you elaborate a little more on what's happening or the specific text of any diagnostics you're receiving?
Now if Tomcat is running and you're trying to reboot, for instance, then you'll probably want to shut down Tomcat first, or rework the shutdown to perform that shutdown automatically.
If you're intending to run Apache Tomcat and don't want that icon to appear in the Dock, then you'll want to use a command-line editor or TextWrangler text editor (do not use a GUI text editor, Office, nor the TextEdit tool, to edit this file, as these will convert the file to a format that won't be readable by the Unix environment) the catalina.properties file, and add the following configuration setting:
java.awt.headless=true
On a local 10.6 OS X Server box, here's the path to that file:
$ locate catalina.properties
/Library/Tomcat/conf/catalina.properties
$