Pekerman, asked specifically about the incident in the tournament opener and his view on a potential introduction of a video challenge as in tennis, said refereeing errors were human but they came at a cost to teams and fans.
"I think that so far FIFA is trying by whatever means to cope with situations which create controversy," the Argentine told reporters.
"Many situations have been resolved nicely in the past but there are perhaps certain elements pending and the fans and the teams sometimes suffer a lot when a serious mistake has been committed."
Croatia and Brazil were level at 1-1 on Thursday with 20 minutes left in the game when Brazil's Fred went down in the box.
Japanese referee Yuichi Nishimura ruled that Croatia's Dejan Lovren had fouled the striker, who looked to have gone down without being seriously challenged.
Neymar converted the penalty for his second goal of the game and the hosts went on to win 3-1 with Croatia coach Niko Kovac calling it a "ridiculous" decision and warning that such calls could turn the World Cup into a "circus".
"This means that we should be ready to cooperate in what ever is possible to be more efficient when it comes to taking decisions," Pekerman said.
"We also have to accept at the same time that the match for coaches referees and players will be marked by human error."
FIFA President Sepp Blatter suggested this week that a manager or coach could be allowed to challenge up to two refereeing decisions during a game.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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