City came from behind to secure their 13th consecutive win the Premier League this season against West Ham United on Sunday and re-established an eight point advantage over United, who briefly closed the gap on after their thrilling win away to Arsenal.
The Premier League leaders were made to come from behind however against David Moyes' side after they were undone by a routine corner kick just before half-time, with Angelo Ogbonna's header giving the visitors a surprise lead.
Goals from Nicolas Otamendi and David Silva ensured City's winning run continued but the manner in which the hosts conceded concerned Guardiola, with Michail Antonio coming within inches of scoring from a similar routine earlier in the first-half.
United's three summer signings in Victor Lindelof, Romelu Lukaku and Nemanja Matic stand at 6ft 2in, 6ft 3in and 6ft 4in respectively, with Eric Bailly, Paul Pogba and Zlatan Ibrahimovic helping make United the second tallest squad in the Premier League.
Guardiola acknowledges that United's height is his biggest concern heading into the derby, telling BBC Sport: "It was similar to the last few games, in the second half I thought we would score. It was massive. They played 10 players inside the box, it was almost impossible. It's a big victory. It showed what we are.
"You have to try to solve it [when teams pack the defence]. We had two strikers in the second half and that helped, it was a big lesson for me. We created more with two.
"The pace was better, we had more presence in the box. Kevin de Bruyne playing as the holding midfielder gave us the tempo. We were much, much better.
"We spoke a lot about defending set-pieces but they are taller. It will happen again next week against United so we have to try and concede fewer set-pieces."