Pep Guardiola's side started its title defence with an emphatic victory at London Stadium courtesy of goals from Gabriel Jesus, Sergio Aguero and a Raheem Sterling hat-trick.
Hammers manager Pellegrini felt his players were too "innocent", especially in the first half, as they conceded too many simple free-kicks when in promising positions.
"Every time we tried to arrive in their box they committed fouls. We were innocent in that regard," he said.
"If you review the game, that is why we didn't create too many chances in the first half. All our offensive moments of attacking ended in a foul. You can look at the statistics. They committed 13 fouls, we committed five. But that wasn't the reason why we lost."
According to Opta data, West Ham conceded six free-kicks to City's 13, but the visitors led 8-1 in terms of fouls committed by half-time.
Kyle Walker and Sterling were the only City players booked, with Mike Dean handing out those cautions in the 87th minute and three minutes into second-half stoppage time.
It is not the first time City have been accused of such a tactic. Last November, former Manchester United captain Gary Neville said Fernandinho in particular was happy to foul to stop counter-attacks, prompting Guardiola to respond: "Never have my teams been focused on doing something wrong against the opponents."
Guardiola was riled again in April when Ole Gunnar Solskjaer suggested City would be happy to give away free-kicks to halt United in their tracks in the derby. "I never prepare a game in 10 seasons as a manager thinking about this kind of thing. Never," he said.
Pellegrini felt City's approach to stopping West Ham attacks was one of the main differences in a balanced first half, but he insisted he did not think it the only reason for his side's humbling defeat.
When asked if he might encourage his players to adopt the same tactic, he said: "We must be more intelligent though to know when to make [fouls], not use it as a system.
"If you review the game, we didn't create too many chances because many of our attacking chances were stopped by a foul.
"But I repeat, I don't think that is just the reason we lost 5-0."
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