Striker James Keene, who joined the Harriers on loan from Portsmouth, played against Bristol Rovers and Chester in October.
A Football League disciplinary commission has imposed a £6,000 fine and a second £6,000 fine suspended for two years with Harriers also meeting the cost of the hearing.
Chairman Colin Youngjohns said: "We're satisfied we had a fair hearing before the commission and we've accepted their punishment.
"Steps have been taken to ensure this type of administrative error never happens again."