I don't think you can tell what the source is. Suppose your relationship with the person who reacts to you negatively is one in which you're free to actually sit down and discuss the issue at great length and in great detail. Suppose you and the other person are both capable of that sort of intense discussion and willing to keep at it doggedly until every aspect of the question has been explored. Even in that ideal situation, you're still unlikely to identify the source -- for the simple reason that people who react negatively to you will rarely know why they're doing that. Even when you're willing to ask and they're willing to tell you, even when their intention is to speak the truth, even when (as is usually the case) they're convinced that their words are the truth, you can't rely on what they say. That's neither their fault nor yours, it's just the way things are in this real world. Unless you're a skilled psychotherapist, working to identify the specific source of the reaction is a waste of your time and energy. But there are a few things we know that are helpful, all the same.
1. Suppose X reacts negatively to Y's appearance -- to Y's weight or height or the way Y is dressed, or something of that kind. When Y has good verbal and nonverbal communication skills, the reaction will be temporary. X will soon forget all about that initial reaction.
2. Suppose Y keeps saying the wrong thing, time after time; the chances are pretty good that X will become angry enough to complain about it, which will bring the problem out into the open where it's possible to at least try to resolve it.
3. But if Y's body language is a constant source of confusion or irritation, it's possible for years -- even a lifetime -- to go by without either X or Y ever knowing that that's what's wrong.
I've been dealing with the "people react negatively to me" problem for more than a quarter of a century. My experience with the problem is extensive enough that I can sometimes quickly identify what's triggering the reaction. [An example would be the man I wrote about previously, who got nothing but negativity and hostility from his male employees because he was operating out of the Traditional Schoolroom metaphor and the other men were all operating out of the Football Game metaphor. That one was immediately obvious just from his description of what was happening and from his speech patterns. (It's almost impossible to keep NVC problems and metaphor clash problems separate, because so much of your nonverbal communication is determined by your choice of metaphor.)] I've worked with such a wide array of situations where males are reacting negatively to females in the workplace that I know those patterns well and can often identify the probable triggering factor(s). It's easy to spot the source of trouble when it's caused by interactions between a touch dominant person and people who are sight or hearing dominant. But beyond that -- based not on controlled scientific studies but only on experience -- I'm comfortable saying that for American English it's best to fall back on the default hypothesis: that the most likely cause of serious negative-reaction problems is one or more nonverbal communication factors.
[Final note: When the factor that triggers the negative reaction is the voice -- the voice quality, voice tone, intonation -- fixing that to even a minor degree will always improve matters and is always worth the investment. I've had dozens of women clients who faced constant negative reactions for just one reason: Because their voices sounded like the voices of small children, people treated them like small children. Power dressing won't fix that; plastic surgery won't fix that; the most exquisite choice of words won't fix that. It's the voice that has to be fixed.]