The plugin will backup the current WordPress installation in its entirety so if it has multiple sites it will back them all up as one. We don't currently support individual site backup for multisite installations - we treat it as a single installation. No plans to support that yet as it introduces a lot of complexity.
So as long as the sites are separate wordpress files with the plugin installed separately it should work fine. Maybe you are ticking "Backup the WordPress parent folder" in general settings? It's would make it back up other things as well as the current WordPress installation - and this could mean other wordpress installations too (although the feature isn't supported for that purpose! It's only intended for backing up static HTML websites where the blog is in a separate folder such as /blog/.)
Databases for each WordPress should be separate too. If they share same database, might need to adjust settings to not backup all database tables.
Let me know if you still think things aren't working as they should. And provide some examples of paths of the installations on the server etc and if you do have the backup wordpress folder enabled.