You can use the --q option to force a specific series by numeric ID. However, you may prefer to use the --filter option to include / exclude episodes in a more generic / automation-friendly manner.

e.g. query by series ID:
--q 95451
e.g. include / exclude by series name:
--filter "none{ n ...

I run Filebot on both Windows and more commonly, on a Linux host running Ubuntu 18.04.

It works 95% of the time on Linux, but every now and then I have this weird problem where in a given directory, some files are randomly given a different series title to others. I encountered it this morning ...