I have a quote from Paul which says Yoko told him one of the first times he hurt John was when he went off to do the "Family Way" without including him. He said he didn't think about how it could have hurt him since he just thought of it like a "In his Own Write" type of project (Paul thought of the title to John's book, by the way and helped on parts of it)
The problem with John and Paul were the way they handled things, especially when they should have communicated their feelings. John would tend to be silent and just not say anything and it would boil to the surface later- Paul would just pretend it wasn't happening and ignore problems and hope they solved themselves- not a good combo between the two of them- by the time it got to where they had to face the problems, it was too late to work out all the years that had accumulated. Plus, with Yoko by John's side at all times, it was impossible for Paul to talk to John privately, which his pride might not let him be as honest as he would if he and John were alone together. Paul admitted he did like to go to John with songs to work on after Yoko came on board because he wanted them to work alone and she intimidated him because he felt he had to be "clever" or "avant-garde" with her by John's side- so instead, he just withdrew from doing it.