When a file is checked out, on-access scanning quarantines the same file many times. In addition, SharePoint is not substituting the removed text with the 'Replacement text', which is what usually happens when a document is found to contain disallowed text.
Each time you try to download a file that has either been blocked or has been replaced/cleaned by on-access scanning, the file is scanned again.
The SharePoint 'Virus Found' window reports 'The file was cleaned and may now be opened on your computer.' This message loops: each time you click 'OK' to this message, SharePoint scans the file again and a new instance of the blocked file is placed in quarantine.The side effect is that if we have chosen to quarantine the item, then we quarantine the item multiple times.
What to do
There are two possible causes/solutions to this issue: