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Dons fans queued for over 24 hours in an attempt to secure a brief for the big game at the end of the month, but many were left ticketless.
The problem is thought to be because Spanish teams are not used to large travelling supports for UEFA Cup games.
But the former Dons captain and gaffer says that the club is trying its hardest to ensure fans are not left disappointed.
Willie said: "We will push Atletico for a higher allocation but ultimately it is their home game.
"Hopefully we will get more but at this late stage we cannot make any guarantees."
And Willie refused to admit Aberdeen had no chance of qualifying from the group after the disappointing draw against Lokomotiv Moscow.
He said: "I am not ruling out the chances of shocking Madrid.
"A draw in Spain would put us in a strong position to qualify."