I think a lot of that to do with the way his character is being set up, especially in contrast to the other Avengers.

Of all the characters with an arc in Civil War, Vision is the only character whose emotional perspective is never discussed. Wanda talks about how people feel about her and how she feels about herself; T’Challa expresses his feelings on vengeance and letting go; Tony talks about his guilt and his desire to keep his family together, etc. 

But since most of Vision’s dialogue is about logic–what he thinks has, is, and will happen based upon his understanding of the facts of the situation–the audience is left to their own interpretation. There is only one instance, in my opinion, in both of his movies where Vision expresses what is clearly emotional motivation–

Despite that, the writers tried to be as clear as possible that Vision has trouble detecting social cues and emotion in other people–his introductory scene in Civil War really smartly sets it up. 

Not only does it establish Vision’s unfamiliarity with social customs, they take it a step further by telling us even though Vision doesn’t understand these social rules, he still attempts to respect them to the best of his ability. That’s the point of this bit right here:

This line is meant to tell us that Vision intended to respect Wanda’s desires, but that their previous discussion (”We talked about this!”) led him to believe that the layers and caveats about privacy were different than how Wanda sees them. 

This scene sets the tone for all of Vision’s scenes: that even though Vision does not intrinsically understand, he makes an effort to learn. His understanding and experiences are very different from the rest of the characters, but he is by no means malicious or even unthoughtful. 

If Infinity War chooses to expand on Vision’s perspective of emotion I think it’ll be easier for audiences to understand. Until then, all those things that assign Vision a malice that isn’t there–that Vision was trying to manipulate Wanda into staying at the compound; that he was trying to blame her for the “catastrophe”; that he purposefully shot Rhodey down in anger, and so on, will persist.