Hi there,
If you want to ignore the downloading of trailers you can simply add the "--no-trailers" option and they will not be downloaded. In regards to some files not being cataloged, this could be due to three reasons: The specific video title entry may not yet exist yet in the database, The video file is using an uncommon video extension (Not avi/mp4/mkv), or there is a unique issue specific to your environment.
If you can provide me some sample video file names your using, I would be happy to try and reproduce what your seeing and see if I can find you a solution! Any details, steps, or screenshots showing what your doing would help as well!