The Japan international was a junior with Barca before he was forced to return home as part of the club's FIFA punishment for breaking youth recruitment laws. Kubo returned to Spain last summer by signing for Real Madrid before being loaned to Real Mallorca this season.
Vila told AS: "It is one of the big mistakes the club has made in the last decade. We are going to regret to have let Kubo escape and have left him on a silver platter for Real Madrid.
"Yes (it is serious). It is an improper mistake of a club like Barcelona.
"Letting out such a talent is very serious, but even worse if it is a striker, who are highly coveted and sought after pieces on the market."
Vila added: "He's not afraid of anything. He lacks a bit of physique. He is not very tall. But otherwise, he is a very well-developed player. With the talent and intelligence to be among the best in the world very soon."