• a module has 4 web facets (because I'm obliged to have different web.xml for local, test and production config)
• when debugging I deploy the "dev" facet (i.e.: this is the facet enabled in the "deployment" tab in the debug config)
• the other facets are NOT checked in the "deploy web facet '<facet-name>'
• for one of them (the "test" facet) I had "create web module exploded directory" enabled in the "Java EE Build Settings"
• the directory was the same as for the other facet
• when starting the deployment, the resources from the "test" configuration (i.e. the ones coming from the dir resulting as "web resource directory" in the "test" configuration are copied on the web module exploded dir

I think that only the resources for the deployment module should be copied.