I am bumping this old thread because I am having the same issue since updating my vlc. Videos in the portrait mode seem to have a problem with not being able to crop, zoom etc
Video files that look like they have a camera film on the icon work (see 1st picture), whereas all the files that do not have a film (see second picture) on the icon do not work.
Have not updated in a few years, and since doing so, when cropping a video, it stretches it instead, and also the colour, saturation, brightness etc is really off. I don't know what is causing this issue.