Given the dependency is published with ivy like:

<publications>
    <artifact name="kafka_2.10" type="jar" ext="jar" conf="archives"/>
    <artifact name="kafka_2.10" type="jar" ext="jar" conf="runtime"/>
</publications>

Gradle internally in the cache creates ivy file like:

<publications>
    <artifact name="kafka_2.10" type="jar" ext="jar" conf="archives"/>
</publications>

Symptoms:

1. Runtime errors, compilation errors: the artifact file is missing from the configuration.files (the dependency is correctly resolved).
2. The artifact file is present in configuration.files only when --refresh-dependencies flag is used.

With Gradle 1.12, gradle translates ivy file into:

<publications>
    <artifact name="kafka_2.10" type="jar" ext="jar" conf="archives,runtime"/>
</publications>

This error hard to figure out by the end users because missing artifact manifests in runtime or at best compilation errors and dependency reports show that the dependency is correctly resolved.