When using the GUI to scan multiple files at once, all of the output files take the name of the first item in the list. There's currently no way to alter this behavior in the GUI besides manually scanning each file at a time. There's many reasons this is inconvenient, especially for organization or reference purposes.
It would be preferable if, by default, each output file took its names from the file it's respectively trimmed from. Perhaps also some various options for how the user would like the output files to be named.