Ten Hag said Haller's name was on a computerized list of players but a box next to his name was not checked when it was sent to UEFA.
“It's a mistake that should not have happened,” Ten Hag said, adding: "“Never a dull moment in Amsterdam. Of course, he is unbelievably disappointed."
Haller joined Ajax from England's West Ham in last month's winter transfer market.
Ten Hag was previously Haller's coach at FC Utrecht. The Ivory Coast striker moved to Eintracht Frankfurt in Germany before joining West Ham in July 2019.