filevault-package-maven-plugin wrongly reports duplicate files for same path

I have the following setup:

• a maven plugin generates css files from scss files in the src/main/content/jcr_root folder, add's them to target/vault-work/jcr_root/...
• maven resources plugin adds all the other files that are in the src/main/content/jcr_root to the target/vault-work/jcr_root
• filevault-package-maven-plugin creates the package, with as settings jcrRootSourceDirectory = 
  ${project.build.directory}/vault-work/jcr_root

When doing this, the filevault plugin throws errors on duplicate files, for example:

Found duplicate file 'jcr_root/apps/author/websites/general/css/_header.scss' from sources 'target/vault-work/jcr_root/apps/author/websites/general/css/_header.scss' and 'target/vault-work/jcr_root/apps/author/websites/general/css/_header.scss'

As you can see, this is two times the same path.

I'm not sure if this is fixable through different plugin configuration? I can make a PR that checks if both paths are the same before logging as duplicate file, but that just sounds like a workaround instead of a correct fix