In John's gospel, the technique of relating a misunderstanding is often used to lead to a point of decision. For example, a group of Jews misunderstood Jesus' words and decided to reject Him (Jn 8:59). On other occasions, people misunderstood Jesus, yet decided to accept Him (see e.g. Jn 4:11ff).
Many misunderstandings occur simply because Catholics don't know their faith. God has blessed us abundantly with the clear teaching of the Church in her Bible and the Catechism of the Catholic Church. Praise God for the Church! If we don't take the time to know the teachings and expectations of living our faith, we have no excuse for misunderstanding God in those areas (see Catechism, 1791).
Are you misunderstanding the Lord about something not spelled out clearly in the Bible or the Catechism? It may be you can't understand in which direction God is leading you — to move, marry, accept a religious vocation, change jobs, or join a small Christian community, etc. As He did in John's Gospel, Jesus may be allowing this time of misunderstanding so He can work in you a far greater good than simply trying to lead you to make the right choice. He may be using your misunderstanding to give you the opportunity to accept Him as Lord of every aspect of your life.
Getting it right is important. Getting right with God is even more important. Misunderstand perfectly. Decide to accept Jesus and allow Him to lead you through the cross of misunderstanding into His perfect will for you, however long it takes.