Yes ".bc!" files are bitcomet incomplete downloaded files. The bitcomet placed an extension to the files until it is completed. Technically it should not be detected by Jav-it as a movie file. Apparently Jav-it still detects it as movie file which is a bug. The multiple files are created by Jav-it using a single command. Those ".bc!" files get downloaded with "*.mp4.nfo" or "*.mp4.tbn". Subsequently after the files completed download by bitcomet and changed to .mp4 extension, running Jav-it the second time on these files (using the same command) will download additional files with "*.nfo" or "*.tbn". Plex do not add extra files to the import. Ideally stopping Jav-it from detecting ".bc!" extensions or any other extension other than movie extension will solve this issue.
I only use this command, jav-it.exe catalog -d u:\Downloads --alt-naming-method="original" but it will come out multiple files from the same set of movies. For example "KCDA-296.mp4.bc!" was the initial file, running Jav-it will get "KCDA-296.mp4.nfo". Subsequently "KCDA-296.mp4", when running Jav-it again will have "KCDA-296.nfo".
Yes under alternate naming conventions with Jav-It, existing cataloged files under different naming conventions are not removed is correct, but I'm using the same naming convention. Extra files still get generated but with a "*.mp4.nfo" naming.
As for missing titles, I have no idea how to reproduce it because it happens randomly. I will try to delete all the files using your method and try to generate with a clean base and see how it goes.