A few possibilities,
The user refreshed the page before the upload was complete.
The user's internet connection cut-out or hiccuped during the upload.
If you're using PHP ( im guessing ) check the following settings in your php.ini.
max_execution_time
If the script takes too long to execute, the server will stop it based on this setting.
max_file_uploads
If the user tries to upload more files than this setting at once, then that might be the cause.
upload_max_filesize
If any of the files are larger than this setting, the file wont be uploaded. This can be handled before it hits the server on the client side with:
Sorry, but without more specific information, I can't narrow it down any further.
If it's only affecting 1% of your users, that's acceptable in my opinion ;) Personally I wouldn't waste time fixing a bug for the 1% unless its the client.