During the closing stages of the clash at the Stade Velodrome, Neymar reacted to a challenge from Lucas Ocampos, prompting the official to hand the Brazilian a second yellow card.
However, Emery has disagreed with the decision, suggesting that referees should be doing more to protect players who wish to play football
The 45-year-old is quoted by the Daily Mail as saying: "We are a little disappointed about the sending-off because he was fouled a lot throughout the match. I think the referee [Ruddy Buquet] also needs to think well. We must protect the players.
"The yellow card, I think it's not fair to Neymar. He's a player who wants to play, but if every game he is provoked, [there will be] aggression. I think it's a job to protect the important players in both teams."
After the match, Neymar claimed that the referee's call was "unfair".