Guardiola clashed with Liverpool fans after Phil Foden's 53rd-minute goal was disallowed due to an earlier foul from Erling Haaland.
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It later emerged that the City boss was being targeted by some Reds fans behind him on the Main Stand, however, none of the objects struck him.
Liverpool have condemned the 'totally unacceptable behaviour' and have opened an investigation into the matter.
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A club spokesperson said: "We are aware of an incident involving objects being thrown into the technical area at today's game.
"This is totally unacceptable behaviour and not the standards of behaviour we expect at Anfield.
"This incident will be fully investigated using CCTV and those found guilty will be punished, including a lifetime ban from Anfield Stadium and a possible football banning order."
It is not the first time there has been crowd trouble around games involving Liverpool and City at Anfield, with the rivalry between the two clubs having grown considerably in recent years.
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Most notoriously, in 2018, City's team bus was pelted with bottles and other objects as it arrived at the Merseyside ground for a Champions League encounter.
Asked about the latest incident, Guardiola said sarcastically: "Next time we will do it better. It didn't get me. They try it again next year.
"All these coins, they tried, but didn't get it. They got the coach years ago."
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Opposite number Jurgen Klopp had not been aware of the matter but apologised on behalf of the home club.
He said: "Oh, horrible. I am sorry. I apologise for that. I had no idea about it. It never should happen, never."
It was not the only unsavoury incident on Sunday with Liverpool also expressing their disappointment at chanting and vandalism by City fans referencing 'chants relating to stadium tragedies.'
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While there was chanting during the game, graffiti was also left in a number of areas of the Anfield Road End, which houses visiting supporters.
The PA news agency reports some of the graffiti referred to 'murderers' and the number of people killed at both Heysel and Hillsborough.
A Liverpool statement read: "We are deeply disappointed to hear vile chants relating to football stadium tragedies from the away section during today's game at Anfield. The concourse in the away section was also vandalised with graffiti of a similar nature.
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"We know the impact such behaviour has on the families, survivors and all those associated with such disasters.
"We are working with the relevant authorities in order to do our utmost to ensure these chants are eradicated from football altogether."
Guardiola also bemoaned the decision to disallow Foden's strike and lamented the mistake which led to Mohamed Salah's decisive goal.
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Speaking to the BBC, he said: "This is Anfield, every time you come here lately unfortunately this is Anfield.
"We played a really good game but this is a game where there are really fine margins and the mistakes are punished.
"We made a mistake and we cannot concede and that's why we lost the game.
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"We played to beat Liverpool today, definitely we played for that. After 1-0 the crowd shouted but we shouted more on the pitch.
"The referee said play on, play on, play on, there were a thousand million fouls like this and this one is because we scored a goal.
"So they disallowed because we scored a goal, otherwise it would not have been disallowed. We lost because we make a mistake but this is Anfield."