There have also been calls to move semi-finals away from Wembley to another neutral venue.
The club laid on 12 coaches but road closures because of the Manchester marathon made it complicated for supporters to meet at Etihad Stadium for the 09:30 departure, while some did not arrive back until 01:30 on Monday morning.
Had the match gone to extra time or penalties, it would have made it even more difficult for City fans to head home, with only three trains to Manchester departing Euston Station after 20:00.
"One day maybe the FA Cup will be played here in the north," City boss Guardiola said in his pre-match news conference on Friday.
"They will come here to Old Trafford or [the] Etihad or Anfield or Goodison Park. I understand the people, I'm not the person to say.
"All around the world people suffer economically and I understand completely it's not easy for them."
Nick Clarke, a founder of the MCFC Fans Foodbank Support, told BBC Sport that City are "a northern club" and it is a 400-mile round trip for fans.
Clarke said he was "out of pocket" for the outing as he booked a 16-seater minibus for £850 which was only taken up by 12 people, while his ticket cost £45 and the total for food and drink was £60.
BBC Sport asked City fans their thoughts with Steve saying semi-finals at Wembley take the "aura" away around those matches, Andrew asking for a "geographically sensible ground", while Ian said the costs "mount up".
However, Wembley is the home of the semi-finals and can accommodate the greatest number of fans for the clubs competing in the last four.
Sources say talk of a neutral ground, say in the north, is easy to mention but difficult to organise because April is a busy period for Premier League clubs who might host the semi-finals.