Raheem Sterling scored a hat-trick but half a dozen delays for video technology referrals overshadowed the London Stadium encounter.
Gabriel Jesus had a goal ruled out when Sterling’s shoulder was marginally judged offside.
“We lost a little bit, the instant?” said Guardiola.
“You have to celebrate it when it’s so clear, when there’s doubts, celebrate it but always be focused because maybe it’s not regular and you have to continue your concentration to not lose our momentum.
“After what happened against Tottenham in the quarter finals, where we have scored in the 95th minute and we were there.
“All the 60,000 in joy, dancing, jumping and one second later, we lost because it was offside – now I’m used to live these situations.
“The passion, now we can control that emotion. You have to be mentally strong when VAR is not on our side. It will be a good lesson for our future.
“The only thing I wish is that VAR doesn’t make mistakes.
“My only concern is when VAR makes a mistake and after that happens quite often, it’s better that referees make the decisions and always we live with them.”
West Ham boss Manuel Pellegrini said: “It is not easy to get used to it, but I think the result will be fairer if we use it in the right moments.
“Football is so fast today it is impossible for referees to see all. It will improve football.
“If it is for an important mistake, then maybe. If you are going to use it for every corner, you will find four penalties.”