Organizational creation is messy - period, pretty much regardless of size. The only exceptions are when a very strong leader is almost dictatorial and ruthless, and even then it often isn't clean and precise at the beginning.
This is true especially of "revolutions" - where "recruitment" of others from existing organizations occurs. Everyone brings their own ideas and biases and perspectives to the table, and it takes a lot to work out how the organization should be built and function. Strong leaders want their own ideas implemented, and things are a bit chaotic until a consensus is reached.
The LDS Church is one of the best examples of this in existence, frankly.
When you look closely at all of the elements that existed (and they are legion) - and the overall philosophy Joseph employed (correct principles and self-governance encapsulated in a Zionist organizational philosophy that reacted only to extremes, essentially) - and his willingness to try just about anything (literal speculation and experimentation almost without limit) - and the compilation of the early church membership as exclusively convert-based (with all of the differing beliefs even the leaders brought to the new church) there really isn't any other result that makes sense than free-flowing messiness and on-going conflict. That only stopped when a more authoritarian leader like Brigham Young took the reins in geographic isolation.
For those who can't "see it" at the macro-organizational level, look at marriages. Often, the first few months or years consist of trying to figure it out and make it work, while those that last for over 5-7 years often settle into a comfortable pattern - which then becomes an issue after about 20 years, when one of the partners begins to want some of the excitement that existed at the beginning. It's a natural, human pattern no matter the size of the "organization".
Finally, read Jacob 5 with this issue in mind. It's quite direct in its description of the inevitability of "pruning wild fruit" being a historical constant.