Consider the attached multiproject.
The root project has a runtime dependency on projects A and B.
However, the war task depends on a custom task.
This custom task (which is then executed before the war) itself depends on the production of the JAR of a custom configuration of B: this JAR is marked with "custom" classifier.

On the other hand, A has a compile dependency on the custom configuration of B.
So, when the war task of the root project is invoked, in the WEB-INF lib of the resulting WAR I find:
A.jar
B-custom.jar

However, since the root project explicitely depends on project B (default configuration!), I would expect to find B.jar in the root project war too!

In real-world cases, if B-custom.jar is a stripped-down version of B.jar, the resulting war has an incomplete classpath.