Chelsea and Manchester United face club versus country rows over Hernan Crespo and Cristiano Ronaldo.
Argentina have hit out at Chelsea's treatment of striker Crespo while Blues boss Jose Mourinho is angry at the international fixture calendar.
Meanwhile, Portugal coach Luiz Felipe Scolari is adamant he will not be told when to use United winger Ronaldo.
Mourinho said: "National teams prepare in such a disparate way that it's hard to find criterion beyond criticism."
He added: "Once more there is confusion, once more I have my heart in my mouth.
"It was with their national teams that I lost Claude Makelele, Asier Del Horno, Damien Duff and Arjen Robben.
"That's without looking further back and at last season when Paulo Ferreira also had to undergo surgery.
"England seem intelligent to me. They think about the burden constituted by the Premiership and opted for just one game, in Europe, but against a South American opponent, in this case Argentina, who could offer them a different playing style.
"For their part, Argentina were looking for a European opponent with a different playing style to those it meets in South America.
"But then they are going to Qatar, returning their players to their clubs one day before the weekend's competitions.
"The French play two games and, incredible as it seems, they go to the Caribbean, obliging players such as Makelele, Thierry Henry or Patrick Vieira to make a journey of many hours and to a complete change of climate."
Pekerman played Crespo from the start against England and the 30-year-old scored his country's first goal in the 3-2 loss before being taken off with after 70 minutes with a calf injury.
Crespo has missed the last two games for Chelsea against Real Betis and Manchester United and there are reports he was involved a row with Mourinho.
Pekerman said: "It's difficult to understand a world-class striker not playing very often. Of course I'd like to see him sharper and fitter in a World Cup.
"It was a strain injury to his calf. It came through not playing regularly, without a doubt.
"If he was fitter and playing regularly that would not have happened.
"It's still early in the season and we've spoken about it but I only hope now he plays more games for Chelsea for the rest of the season."
United are believed to have wanted Ronaldo used sparingly against Croatia and Northern Ireland.
But the winger figured for 75 minutes against Croatia and is set to play against Northern Ireland.
Scolari said: "Perhaps I should say 'these are only friendlies, don't try too hard - don't get injured - then you can all go back to your clubs in perfect condition'.
"I'm fed up with people trying to pressure me about who I pick."