Why is cultural understanding often wrong? One common set of beliefs that I time and time again find wrong are the 'cultural norms' that are taught to people as if to make them more educated about differences in behaviors across cultures. 


In Asia, it is often believed by Western-educated individuals that averting eye gaze is a show of respect. On the contrary, it is naturally a human instinct that eye contact will serve to establish emotional bonds between people. Without eye contact, people will lose a lot of the natural opportunity to connect between people. In this sense, eye contact is inherently not differently understood depending on culture, but rather a common language hard-wired into our neurological anatomy. It is also wrong how people think prolonged eye gazes are rude in Asia only -- it is rude in America as well. Nobody likes to get stared at, whatever the intentions. 
So it follows that if an adequate eye gaze is indeed understood as an affront, then it is the necessity to preserve hierarchy that is preventing meaningful connections being made between persons of differing hierarchies. In my country, South Korea, there is a lot of discussion of how the society as a whole lacks communication -- between political factions and individuals in the family. No wonder! Compounding the problem is the fact that hierarchy and language are also correlated -- the honorific system is extremely complicated compared to any other Western language. 
In the same way, Asian hierarchical culture is not a difference, but more often than not a problem. It is a genuine hindrance to democratic ways of life. When often western modes of behavior, like the fact that it is okay to walk out of a lecture hall, or put legs atop of a college style desk-chair combo, or to address professors by their name, are arguably examples of when liberty goes too far, there is in Asia, the contrasting draconian rules on the other side of the spectrum. Ageism -- the belief that age translates to authority, is one of them. Most companies prize experience over education -- unless the experienced are also well-educated. An attachment to external validations, like credentials, are super important. 
To refer to the book "The Geography of Thought", therein the author makes a distinction between the 'weak dialectic' versus the 'linear logic' that Westerners use. I think this is less a cultural difference as it is the result of the Enlightenment and the formal logic developed by specific Enlightenment figures. The book argues that Asians who are expatriates or who have a PhD use linear logic more heavily. This already serves to prove that logic is borne out of a different intellectual history, rather than simply being a product of culture. In other words, intellectual styles are the result of a specific process that was unique to the Western world.
I have a little difficulty understanding your question. are you asking why do we percieve slightly different behaviors as culturally different? I would say that for me cultural difference is a continuum or degree rather than difference. For example, as you wrote, prolonged eye contact is rude everywhere, but how much is acceptable might be different. Also for me the source of difference doesn't make it not culturally different. Every cultural difference comes from a source, socio-economic, geographic, historical etc. The different intellectual developments led to some cultural differences at least that's my opinion. Of course we can discuss if we should focus on differences or similarities among human groups. I would say should we choose between. I hope that was what you were asking.
P.C: to be honest, I was thinking about my own experiences and observations but when you think about one of the most popular theories about culture, Hofstede's four dementional theory, sees cultures in a continuem of four dementions (tolerence for uncertainty, individuality-collectivity, masculanity-feminaty, power of distance)(Hofstede, 1983).  It is not some cultures avoid uncertainty or seek it, but that some cultures/social groups avoid uncertainty or seek it more than other cultures/social groups for example. 
Hofstede, G. (1983). National cultures in four dimensions: A research-based theory of cultural differences among nations. International Studies of Management &amp; Organization, 13(1-2), 46-74.