"i am sorry that i was misunderstood" is better than "im sorry you misunderstood" because of the pure fact that if you say "im sorry you misunderstood" it may look like you are putting blame(blaming...
Everyone is useful in their own way and if you feel or if someone tells or seems to not understand you try to explain yourself if you feel the need but at the same time be yourself and you don't owe...