Iker Muniain put the visitors ahead from the penalty spot on 34 minutes at the Estadio Benito Villamarin.
But they struggled to seal the result against the La Liga's bottom side, who were reduced to nine men by the hour-mark as Damien Perquis and Lorenzo Reyes were sent off.
Substitute Guillermo's 81st-minute goal completed the win, but Valverde was far from impressed by his side's attacking play.
"I have the feeling that our attack could've done more," he told a news conference.
"Although we dominated, our play wasn't fluid and I felt that they could have drawn even at any given set-piece.
"It was an ugly game, against nine men, we felt like the game was even.
"We took advantage of the misfortunes of our rivals."
