It could be a number of things. Your media may not be named in the style Plex likes it so it may be having issues identifying. Or you may have been having internet connectivity issues and requests may have been timing out, or you may have been getting throttled by the metadata provider.
The one thing I can think of with regards to usb drives is that flash drives usually have pretty awful write speeds. Plus, plex libraries can grow to hundreds of thousands of files easily and to hundreds of gigabytes (especially if you turn on video preview thumbnails). I really wouldn't recommend hosting the Plex library on a flash drive.
With that said, there are no issues with the Plex docker container. Many people use with very large libraries (on ssds mostly) and scans are fairly quick.