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The Chilean had added further fuel to the fire earlier this month, when he compared Chelsea's defensive setup in the 1-1 home draw to Stoke's, before branding Jose Mourinho's side with the same 'small team' tag.
He has since backtracked, however, telling reporters: 'I want to clarify. They played very well here and I didn't think they were a small team. It was our fault not to have chances.
'It is the third time we played against Stoke and we only scored one goal in three games.'
After scoring 156 goals in all competitions last season, the Premier League holders have made a slower start to this season, sitting five points behind table-toppers Chelsea, but Pellegrini insists that he has been satisfied with the club's start.
'If we win tomorrow, yes, I'm happy,' he added.
'The only game we lost was here against Stoke. It was not in our minds that we could lose that game but that can happen in football.
'I think that, in all other games, we play very well.
'It is not good to be five points behind Chelsea but, in this moment, we have one point more than last year. Arsenal was maybe six points ahead of us and we didn't win the first three games away.
'Things can happen, important things, and we will try to continue playing the way we did against Hull.'
Elsewhere, ex-Blues midfielder Jack Rodwell claims his comments warning up-and-coming English talent about moving to the Etihad were taken out of context.
Rodwell was reported to have made the remarks following his £10 million summer move to Sunderland, but the three-times capped international has said in an interview with BBC's Football Focus that he was misquoted.
'I think I got misquoted a little bit in one of the papers saying don't sign for Manchester City, but basically what I would say is that if you're a young player, you want to be playing every week then you've got to make that decision,' he said.
'If you go to Manchester City you might not quite play every week. But I could never say don't sign for Manchester City because I've got nothing but good things to say about Manchester City as a football club.
'I just want to keep playing regularly and hopefully I want to be playing for England, that's the next ambition.'
Meanwhile, City youngster Jordi Hiwula has spoken of his delight at completing a loan move to Yeovil Town until January.
The 20-year-old striker was the top scorer for the club's Elite Development squad last season, earning a new two-year contract in the process, and is hoping to gain some valuable first-team minutes during his League One stint.
'It's my first loan move, so I think it will be a good one as well to get away from home and experience living away, which should be good,' he told Yeovil's official website.
'I know it's a physical league and a lot of teams like to play balls over the top but there are a few times they are trying to play football as well, which Yeovil are doing. They try and play football and that's what attracted me to coming here as well.
'I think three months for the start is good because I can show what I can do and progress from there.
'If everything goes well and the manager still wants me then I would be open to carrying on here.'