Product Version: NetBeans IDE 6.5 (Build 200811100001)
Java: 1.6.0_05; Java HotSpot(TM) 64-Bit Server VM 1.6.0_05-b13-52
System: Mac OS X version 10.5.4 running on x86_64; MacRoman; en_US (nb)

To reproduce:

1) File -> New Project
2) Java EE -> Enterprise Application
3) Accept defaults on the next screen and hit Next.
4) Choose a server (I went with GlassFish v2). Change Java EE Version to "J2EE 1.3". De-select options to create EJB and
Web Application modules (for simplicity). Click Finish.
5) Right-click on your new project, choose "Verify"

Note that verification fails with this error:

Could not verify successfully.
java.io.IOException: Deployment descriptor file META-INF/application.xml in archive [EnterpriseApplication1]. 
cvc-complex-type.2.4.b: The content of element 'application' is not complete. One of
'{"http://java.sun.com/xml/ns/j2ee":display-name, "http://java.sun.com/xml/ns/j2ee":icon,
"http://java.sun.com/xml/ns/j2ee":module}' is expected.
	at com.sun.enterprise.tools.verifier.VerificationHandler.explodeArchive(VerificationHandler.java:296)
	at com.sun.enterprise.tools.verifier.VerificationHandler.initStandalone(VerificationHandler.java:211)
	at com.sun.enterprise.tools.verifier.VerificationHandler.<init>(VerificationHandler.java:109)
	at com.sun.enterprise.tools.verifier.Verifier.verify(Verifier.java:140)
	at com.sun.enterprise.tools.verifier.Verifier.main(Verifier.java:114)
Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.b: The content of element 'application' is not complete.
One of '{"http://java.sun.com/xml/ns/j2ee":display-name, "http://java.sun.com/xml/ns/j2ee":icon,
"http://java.sun.com/xml/ns/j2ee":module}' is expected.
	at com.sun.enterprise.deployment.io.DeploymentDescriptorFile.read(DeploymentDescriptorFile.java:304)
	at com.sun.enterprise.deployment.io.DeploymentDescriptorFile.read(DeploymentDescriptorFile.java:226)
	at com.sun.enterprise.deployment.archivist.Archivist.readStandardDeploymentDescriptor(Archivist.java:480)
	at com.sun.enterprise.deployment.backend.J2EEModuleExploder.explodeEar(J2EEModuleExploder.java:278)
	at com.sun.enterprise.tools.verifier.VerificationHandler.explodeArchive(VerificationHandler.java:285)
	... 4 more

6) Open the application.xml file that NetBeans generated. Line two looks like this:

<application version="1.4" xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/application_1_4.xsd">

7) Change it to this (application_1_4.xsd becomes application_1_3.xsd):

<application version="1.4" xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/application_1_3.xsd">

8) Verify the application again. It is now valid.

Note that the application version number in the config file is also given as 1.4. I don't know if that's correct or not,
but it doesn't appear to cause an issue. Someone might wish to verify it.