Villarreal suffered a shock 3-2 defeat at Huesca in the first leg of their Copa del Rey last-32 clash on Thursday.
Marcelino's side are sixth in La Liga, but they have work to do in the tie against the side sitting 18th in the Segunda Division after a dramatic contest.
Goals from Matias Nahuel and Cedric Bakambu had twice drawn Villarreal level after Luis Fernandez's opener and Fran Merida's penalty for the hosts.
But they had no answer to Huesca's third goal from on-loan Granada striker Darwin Machis, as the second-tier side held on despite a late red card for Christian Fernandez.
It was a tough night for the seeded sides in most of the Copa's other matches, too. Eibar are on the brink of crashing out after being thumped 3-0 at Ponferradina, with goals from Luka Dordevic, William Jebor and Dmytro Khomchenovskyi doing the damage.
Malaga also lost to Segunda Division opposition, going down 2-1 at Mirandes. Roque Santa Cruz cancelled out Alex Garcia's opener, but Lago Junior scored 21 minutes from time to seal victory for the underdogs.
Last season's finalists Athletic Bilbao are on course for the next round, though, after early goals from Kike Sola and Aymeric Laporte gave them a 2-0 win at Linense.
There were two all-La Liga fixtures as Levante drew 1-1 at home to Espanyol after Roger Marti's late equaliser prevented Mamadou Sylla's strike from proving decisive.
Las Palmas came from behind to beat Real Sociedad 2-1 thanks to goals from Asdrubal Hernandez and Hernan, which sealed victory after Bruma had struck first for the visitors.
