If a user tries to upload an exact copy of previously uploaded file, he sees a warning about it, but only after uploading a complete file to Commons. If there are many such files, a user could upload a batch of files about a hour only to understand that all these files was uploaded earlier. How it should work, in my opinion:

• UploadWizard computes file hash on a local machine
• UW sends the hash to Commons and checks for a duplicates
• UW uploads a file only if no duplicates is found on previous step.