For example:

dependencies { compile project('other').sourceSets.main.classes }

This ends up as a module library containing the other project's 'build/main/classes' directory. This should be transformed into a project dependency in the module file (or better yet, in the compile configuration so that this information is available elsewhere).

A similar problem happens within a project too. For example, say I add an integration test source set:

configurations { integTestCompile }
sourceSets { integTest { compileClasspath = configurations.integTestCompile } }
dependencies { integTestCompile sourceSets.main.classes } }
ideaModule { scopes.TEST.plus.add(configurations.integTestCompile) }

Running gradle ideaModule generates a module file containing 'build/classes/main' as a module library. This should be removed, as there is already an implicit dependency on the main classes.