How can I exclude dependencies brought in from other sub-projects?

exclude for dependencies has a little bit another syntax, so try to do it providing the module name, which is equals to the exclude-me-project name, like:

compile(project(":commons:some-other-project")) {
    exclude module: "exclude-me-project"
}

Alternatively, you may exclude all the transitive dependencies for commons project, but it will remove all the deps of the some-other-project project, including the exclude-me-project:

compile(project(":commons:some-other-project")) {
    transitive = false
}