Villarreal boss Unai Emery was left furious by the decision to award Arsenal a penalty as the Gunners' found a route back into their Europa League semi-final tie.
The Spanish side were leading 2-0 before Manu Trigueros was adjudged to have tripped Bukayo Saka in the box with referee Artur Dias pointing to the spot.
Nicolas Pepe converted the spot-kick to give the Premier League side a lifeline ahead of the second leg at the Emirates next week. But former Arsenal boss Emery was angry at the call from the official.