I'm using Ubuntu 12.04 LTS with de_DE.UTF-8.
I'll attach a simple self-contained sample project: the message is caused by a beans.xml file containing nothing but <beans/>. The message disappears when you add the correct namespace definition.
I don't know if the namespace is really required by the CDI spec, but it does make some sense for Weld to complain.
What doesn't make sense to me is that the message disappears when changing the locale.
I copied my sample WAR to domains/domain1/autodeploy and started GlassFish with
LANG=de_DE.UTF-8 bin/asadmin start-domain --verbose
In this case the error message appears. Using any of LANG=de_DE (without UTF-8) or LANG=C, LANG=en, LANG=en_US, LANG=en_US.UTF-8 the message does not appear.
So my original problem description was incorrect, the warning is not spurious, but its presence should not depend on the locale, and there appears to be an issue with resource bundle lookup.