If the unwanted files are in the latest backup version only, you can delete that backup version as suggested by @tophee with the delete command.
If you want to remove a file or folder from all backup versions, use the purge command:
Usage: purge <storage-URL> <filenames> [<options>]
Purges (removes) files from remote backup data. This command can either take a list of filenames or use the filters
to choose which files to purge. The purge process creates new filesets on the remote destination with the purged
files removed, and will start the compacting process after a purge. By default, the matching files are purged in
all versions, but this can be limited by choosing one or more versions. To test what will happen, use the --dry-run
flag.
--dry-run
Performs the operation, but does not write changes to the local database or the remote storage
--version=<int>
Selects specific versions to purge from, multiple versions can be specified with commas
--time=<time>
Selects a specific version to purge from
--no-auto-compact
Performs a compact process after purging files
--include=<filter>
Selects files to purge, using filter syntax