Communication between 2 people will tend towards some misunderstandings at times, simply because that is how things are. Through some arguments, disagreements, quarrels, fights, unhappiness do we then realise and learn. What's important is not be bogged down by those unpleasant feelings, but to tell yourself that you just learnt one new thing, and eliminated a possible source of conflict in the future.

Only through constant communication (and accordingly, misunderstandings at times too) can 2 people get to know each other better, and understand each other's quirks and what makes one tick. It's a transient dip in pleasantness between the parties, but a long-term growth and maturity in the relationship.