I hate that phrase. Oh, how I hate that phrase. To caution someone to not interpret something “the wrong way” is to imply that there is a “right way” to think: the speaker’s way. The phrase assumes a position of entitlement that blames the listener for not understanding the speaker’s intention. But, that’s just it.
To be effective, communication needs to be performed such that all listeners understand the speaker’s message. It’s a two-way street. If someone’s not understanding what you’re saying the way you’re saying it, that’s failed communication. The burden is then on you to figure out how to get your point across, not on the listener to assume what you meant.
One of the most offensive things any intimate partner has said to me during arguments is, “You’re misunderstanding me.” Again, entitlement. I am making a judgment based on the information you have given me. I am not misunderstanding you; we are having a miscommunication because you haven’t provided me the information I need to understand how you reached your conclusion.
One of the best things you can do for any of your relationships — with friends, family, lovers, coworkers, etc. — is to learn how to argue such that you criticize ideas rather than people.
Leave all “you”s out of what you say and only talk about your own situational impressions. For example, “I become stressed when I see dirty dishes in the sink three days in a row,” is a better, non-aggressive way to assertively approach your messy roommate than, “I hate how you always leave your dirty dishes in the sink.” It is less likely to trigger your roommate’s defensiveness because you’re addressing your feelings about the situation without attacking their personhood or behavior habits.
An effective communication style is vital to the longevity of any meaningful relationship, and it’s a lot easier to get your point across when you can do it without alienating your audience. I encourage you to steer away from the “Don’t take this the wrong way”s, “don’t get me wrong”s, and “you’re misunderstanding me”s and, instead, spend more energy crafting how you say what you say to the important people in your life.