You can, of course, just go through every folder, hidden or not, and delete the files that you remember seeing somewhere else. You can dig through your file system and manually delete files, but that's a tedious process. Sometimes, apps download multiple files or folders they need to operate properly.
Find and remove duplicates with Terminal commands.You may also import images you already have in your Photos app, or have multiple video or audio files lurking.
There are times when you duplicate a file to alter it, but never get around to those changes. Having duplicate files on your Mac may not be your fault. Best ways to remove duplicates on your Mac