If someone shows evidence of (1) being generally clueful and (2) having read what you wrote, and they “have missed the points I was making”, then I suggest that you might find it advisable to explain what they misunderstood and how your intention differs from what they thought you said. Just saying “you misunderstood me” achieves nothing. (Unless your only goal is to attack someone who has disagreed with you, I suppose. There may be places where that’s an effective tactic, but I think that here it’s unlikely to make anyone think better of you or worse of them.)
If someone shows evidence of (1) being generally clueful and (2) having read what you wrote, and they “have missed the points I was making”, then I suggest that you might find it advisable to explain what they misunderstood and how your intention differs from what they thought you said. Just saying “you misunderstood me” achieves nothing. (Unless your only goal is to attack someone who has disagreed with you, I suppose. There may be places where that’s an effective tactic, but I think that here it’s unlikely to make anyone think better of you or worse of them.)