S3 backend does have a problem...
I'm using
django-storages' s3boto backend, and when uploading two different files with the same name, the second file will overwrite the first. This happens even if the two files are stored in two different logical folders.
When using django's default FileSystemStorage the files don't get overwritten due to django.core.files.storage.Storage.get_available_name returning a suffixed file name in case of conflict.
Anyways, the S3 backend is the buggy one, not filer. Just be extra careful with how the storage backend handles some of the corner cases...