Atletico did not have a player booked in the second leg, while Barca received one yellow card as well as a red.
Pubill was one of three Atletico players booked in the first leg, when he stopped the ball with his hand after goalkeeper Juan Musso had appeared to restart play with a goal-kick.
Barca complained to Uefa over a “grave lack of VAR intervention” but European football’s governing body said on Tuesday that the club’s protest was “inadmissible”.
“It was tough, especially when you realise you have to work three times as hard to win the match,” added Raphinha, 29.
“I think this tie was quite misleading, in my view. I think everyone can make mistakes; everyone is human.
“But when the mistakes keep repeating themselves in exactly the same way, I think that’s something we need to pay attention to.”
When asked to respond to his comments, Uefa said that its disciplinary body will assess reports from Tuesday’s game before deciding on any next steps, including a possible charge for the former Leeds player.
Atletico keeper Musso said: “You can’t say this match was stolen from them; that’s ridiculous.
“They acted as if they should have had three penalties and we should have had four sendings-off. We won on the pitch, 2–0 away, and when you’re the last man back, you get a red card.”
