Santos coach Muricy Ramalho said that the 19-year-old, who was booked for dissent and then immediately sent off for applauding the referee's decision, cried in the changing room after the incident.
"He has to stay calm even if the referee is wrong," Ramalho told reporters after Neymar became angry over the referee's failure to award a free kick in the 83rd minute
Neymar is expected to lead Brazil's attack at the 2014 World Cup but his style is already the subject of controversy.
Some critics say referees do not give him enough protection, others argue that he goes down too easily and is always looking for a free-kick.
"He is a top player who has his own style of dribbling and he has to get to used to being fouled," Ramalho added.
"Sometimes, he is going to get hunted down. The referee will give two or three free kicks but sometimes they become embarrassed about awarding so many free-kicks.
CHARTER FLIGHT
Neymar was one of several players who returned on a charter flight from Mexico where Brazil won a friendly on Tuesday evening, only 48 hours before Thursday's matches.
Six clubs got together to pay for the flight.
Rever, who also played against Mexico, opened the scoring for Atletico Mineiro after six minutes.
Borges converted a penalty to level for South American champions Santos four minutes after half-time, his 21st goal of the championship.
However, the relegation-threatened Roosters regained the lead with another penalty converted by Magno Alves just before the hour.
Santos, 13th in the table with 38 points, also had defender Crystian sent off.
Fluminense striker Fred, another player involved in the Mexico game, scored a hat-trick but also missed a penalty as the defending champions beat Coritiba 3-1.
His first goal was the pick, as he controlled the ball on his chest and hooked the ball in with a bicycle-kick.
His penalty was saved by goalkeeper Vanderlei with the score at 1-1.
Vasco da Gama came from two goals behind, both scored by substitute Elton, to draw 2-2 at Atletico Paranaense and go level on points with leaders Corinthians, who lost to Botafogo on Wednesday.
Corinthians stayed top on the number of games won.
