Marcelino's men finished with 10 men against Bilbao for the second time this season, and conceded a late equaliser to leave them seven points behind Ernesto Valverde's side in the race for UEFA Champions League honours.
Having bemoaned the late kick-off time for their Camp El Madrigal clash - 10pm local time - in the pre-match, Marcelino's frustration turned to the referee, who left the hosts with 10 men for the final 25 minutes and Bilbao equalised in that period.
"From my position I cannot decide whether it was fair or not. What is clear is that we played two games in this league against Athletic and in both we are left with 10," Marcelino said of Gabriel Paulista's second yellow card.
Aritz Aduriz turned from villain to hero, as his missed penalty in the 39th minute - the lead-up to which saw Paulista pick up his first yellow of the contest - but that was all but forgotten when he equalised seven minutes from time.
Marcelino said it was virtually Bilbao's only chance following the dismissal.
"With 10, the opponent did not create many chances," he said.
"We conceded the equaliser in a predictable move, we were not able to defend it well.
"We had two extra points (taken away) that I think we deserved."
The 42-year-old said catching Bilbao in fourth spot was now unlikely to be an achievable task.
"Fourth place is very far off because Athletic is a very good team with a considerable advantage because it's seven points and goal difference. I think they are clear candidates for the fourth position," he said.
Valverde conceded his Bilbao side was below their best against Villarreal and that 'the expulsion decided the game'.
"Villarreal pressed us well at times and have merit," Valverde said.
"They have great players that anytime can trouble you. It was not our best game but because they also did very well.
"With a man down they dug in and were difficult to reach."
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