Cazorla joined the Gunners in August for a fee believed to be around the £15 million mark and the Spain international has impressed immediately netting seven goals already including a hat-trick at Reading.
Cazorla admitted recently that he would love to face his former club in the final of this year's Champions League, and Pellegrini has revealed that allowing the forward to leave the club was a mistake.
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The Malaga boss told 'Al Primer Toque', a radio show on Spanish station Onda Cero: "There are many clubs who have to give up their big names except Barca or Madrid, so there is a big difference between them [their quality] and the rest.
"Economically, the club had to make a change based on what had been proposed [there was a lot of financial trouble - owner threatened to pull out over TV money] and we had to sell Santi Cazorla.
"Santi's case was inexplicable. It was a time of acute crisis in the club. The departure of Cazorla at the time and at the amount that was agreed was a blunder."
The latest superstar in the Malaga ranks is Isco, who some believe has been empowered by Cazorla's departure, as he has been able to play a more prominent role, a suggestion Pellegrini denies.
He added: "A good player has never benefited from another good player leaving and no player has gone backwards by playing alongside another great player."