There's something about human beings that unknowable. The random girl you saw at the mall (do people still go to malls), the guy you've worked with for years, your father, your mother, your own brother, even yourself - they're all sort of impossible to wrap your head around.
The expressions, reactions, non-verbal queues, etc, that you read are the end result of an internal process that you are never given access to. Then whatever that is has to go through all of your internal processes, filters, biases, before you can come up with any conception of what it means.
So the amazing thing isn't that there are miscommunications. The really incredible thing is that we ever communicate enough to form any meaningful connections or get anything done in the first place. That is the human miracle. Because the more intelligence a group of beings has, the more room there is for miscommunication.
So the next time someone pisses you off in a big way (which, let's face it, will be soon: humans are frustrating and easily frustrated), take some time to really question if the situation means what you think it does. If everyone takes just a little time to do this, then maybe we could communicate a lot more clearly and waste a lot less time. And then we can start talking about the things that really matter.