The plugin only combines scripts on the front-end. Some of the scripts that it finds are only for the backend. There's no way in WP that I'm aware of to differentiate between which files will be in the front-end and which will be in the back-end only since all scripts are en-queued the same and are typically wrapped in a conditional to check for the admin. The plugin is not relying on code execution to find files.
I recommend checking the boxes for all of the files. The list is very big because there are a lot of files that can be combined. Please see the other forum posts on recommended settings and which files to combine.