Body language that comes naturally to some autistic people can be completely invisible to most neurotypical people.
For example, many autistic people respond to questions by nodding their head very slightly. It can feel like a bigger movement than it actually is, and sometimes people don’t notice it. If you’re nodding and people are ignoring you, it might just be that they don’t understand your body language.
Similarly, neurotypical people don’t usually understand the range of things that flapping and various forms of stimming can mean. They tend to read it as distress or as annoying behavior. They don’t usually understand it as body language. Since they lack the skill to understand body language correctly, it can be worth telling them things explicitly.
For instance, if someone doesn’t understand the kind of flapping that means hello, it might be worth saying hello with your voice when you want to greet them.
Sometimes NTs intentionally ignore autistic body language, but sometimes they just don’t understand it.