I think this happens to most of us . I deal with it a number of ways, Sometimes I explain what I meant in the situation when that person is important to me.
So how do you deal with being misunderstood?
There are different kinds of misunderstanding, imo. Some matter, some not. My reaction will depend on the circumstance, and the individual I'm dealing with.
In business, you're looking to make the best impression, so it depends on what the misunderstanding is, and whether it leaves a good or bad impression. Correcting is therefore, optional.
In real-life, if it's someone you care for, and they care for you, then you simply go back to the point of misunderstanding and correct it. It's better when there is open and honest communication.
Also, in real-life, it may be someone you don't like, or you know is difficult to deal with. I have a family member who is this way, he's a right-fighter, so any disagreement has the potential to explode. I found the best way to deal with this type of person is not have any disagreements or misunderstandings at all. This is achieved by never, ever, having contact with them.
In short, it depends on what the misunderstanding is about (important stuff, or casual stuff) and whom you're dealing with. This is ingrained in me very deeply, perhaps because you can't make mistakes in business agreements. So, I tend to be verbose in written communication, attempting to cover every base I possibly can. Such is life.