1. when I add a file, which name is already there, the file is added with a counter (1, ...) added to the filename
That is correct. This ensures that other users do not overwrite other files.
2. when I delete a file, the file is not deleted from the file system
Correct also, but we understand not desired by all. We plan to add some additional options in an upcoming release.
3. group rights are not propagated to the file system, that is, I would expect view and upload permissions for groupmembers would have been set and visible e.g. in the file manager.
Since the preferred and most configuration for Active Social is to not use roles, we then have no way to manage the dnn file system. Also keep in mind that we need to be able to support multiple storage locations (file system, database and cloud). DotNetNuke does not currently support this.
one other thing, when deleting a comment or file, the JS is throwing an error and does not refresh the page
This will be resolved with AS 1.7.2