Marcelino claimed Liverpool pushed the boundaries of the rules as Villarreal lost their Europa League semi-final tie, while suggesting the referee aided the English hosts.
Villarreal saw their 1-0 first-leg lead overturned by Liverpool, who triumphed 3-0 at Anfield on Thursday.
An own goal from Bruno put Villarreal on the back foot early, before Daniel Sturridge and Adam Lallana completed the comeback in the second half.
But Marcelino was left frustrated by Liverpool and the officiating after seeing Victor Ruiz sent off with 19 minutes remaining.
"It was tough against an opponent who played with huge amounts of intensity, maybe on the margins of the rules but the referee allowed it," Marcelino said.
"In the context of this game the referee was letting a lot go, so to then see a sending off against you, you make your own conclusions."
Marcelino did offer credit to the hosts, adding: "We've caught Liverpool in their best form of the season, there's not a lot more to say. They were superior.
"Liverpool played better than us but for all their superiority they didn't create too many chances."