The Brazil international received his first booking before the break when deliberately delaying a Malaga free-kick by tying his laces in front of the ball, before being shown another yellow card in the second half for a strong challenge on Diego Llorente.
The red card was Neymar's first since joining Barcelona from Santos in 2013 and Luis Enrique was not convinced the attacker deserved his dismissal.
"I believe the interpretation of what is worth a yellow card is very special," Luis Enrique told reporters.
"We have to be very careful in some games because there have been strong tackles from behind that did not result in a yellow even though they were clearly worth a booking.
"And then tying your laces gets you a yellow.
"It is very curious that a team that does not play rough gets some incomprehensible yellow cards. Especially when the opponent makes numerous fouls, but does not get a yellow card for it.
"It is curious, but we are used to it."
The red card will keep Neymar out of the upcoming clash with Real Sociedad, but he will be available for the match against Real Madrid unless he receives an additional suspension for his sarcastic applause after being sent off.