Question

Why did the Mormons face troubles with their neighbors in Independence, Missouri?

Answer 1

Because during that period of time Mormons where the only group of people that still practiced polygamy and, still segregated blacks. And they where called trying to alter the original christianity with there own book ( the book of morm)

Answer 2

There are a number of answers to this question, some of which depend on what sources you use.
 
The least debated answers (as to why they faced troubles with their neighbors) I've found in my studies are as follows: Their superstitious beliefs, their isolationist tendencies, and their self-governing ideas. While there is more to be added to this answer, I'll keep it as short as it is.