Often project bins structure and system folders structure mirror each other. After adding new file to system folder, it should be manually imported in project and then moved to relative bin.
There might be a shared folder with media from another editor/vfx artist/sound editor/etc. You will need to check this folder from time to time and manually import new media to your project.
Some files have very complicated names: 132341_NH_134AAB.mp3 When folder gets populated with a lot of files like example above, it is hard to tell which one you just downloaded and you might import duplicate at the end.
Camera folders are complicated as well. Media browser is advised to import media from camera card: it will filter out unnecessary folders and deal with spanned clips.
When rendering image sequence, you should wait for render to be complete and then import it in your project. If you add new files to sequence, you will need to relink project item again.