This error normally means the message file has been deleted from the hard disk (probably by a virus scanner or something else on the PC).
If you can find the message in the VPOP3 settings (Settings → Spamfilter → Quarantine Viewer) and try to open it there. Then, right-click on the window that appears and choose 'Frame Source' or 'View Source' (or something similar) the title bar should show the URL of the page being loaded, such as:
The value after 'msgid=' (beginning with Q and ending with .DAT) is the filename where the quarantined message should be stored.
In the VPOP3 directory on the server disk, there's a folder '_quarantine' with folders inside it. The subfolders are called after the first few characters of the filename (after the Q), so in the above case, it would be 'VPOP3\_quarantine\01d07d6'. In that folder should be the filename you're looking for. If that file doesn't exist, then that's why VPOP3 is reporting the problem. If there's an antivirus program on the same PC as VPOP3, check the quarantine/vault/whatever-it's-called in that antivirus program, to see if the file has been quarantined by the antivirus program.