I don't quite follow what happened. Can you expand a little bit please, perhaps with some examples.

This is easy to reproduce.

I have a multiproject, and I define all libraries we are depending on in a separate file that looks like this:

ext.libraries = [
activeIO_core : 'org.apache.activemq:activeio-core:3.1.2',
(...)
jms_api : 'javax.jms:jms:1.1',
(...)
]

Now, a subproject got a new dependency on jms_api; so in the build file for this subproject I declared:

dependencies {
compile (libraries.commons_collections, libraries.jsm_api,libraries.activeMQ_core)
(...)
}

Please notice the typo "jsm_api" instead of "jms_api"! This caused the reported NPE.

So, my expectation is: Gradle sees the invalid symbolic name and reports it as invalid instead of running into the reported NPE.