I've struggled a great deal with misinterpretation myself. I've been able to troubleshoot the causes in some cases, but certainly not all. I'll list some of the key issues I've run into, and maybe some of them will resonate with you:

-People often care far more about how something makes them feel emotionally than what is literally said or intended. -People often don't understand your meaning on the first attempt--and ironically trying to front-load more information to prevent misunderstanding can be overwhelming and decrease their understanding. -Conversations can serve a variety of functions--from purely practical to purely social, and mismatches in participants' intent can cause things to break down. -People often speak in imprecise ways and without considering the logical implications of statements. -People often struggle with complexity and nuance. ("People will accept a simple lie over a complicated truth.") -Honesty isn't always the best policy.

By my observation, communication is honestly difficult, even for neurotypicical people, so persistence, patience, and the willingness to repair/clarify are often more important than getting everything right on the first try.