The decentralization of authority and use of democratic processes to revise statements of belief and set standards for church leadership has led to some splinters. This usually starts with a social movement such as women’s suffrage that achieves majority support in some congregations sooner than others. The regional or national governing body may then allow women to become elders or pastors based on the desires of the majority (in communion with the holly spirit of course). More conservative congregations would then splinter away from the main body perhaps rejoining decades later when social norms have stabilized across the region or country. Claims are usually made that the split is based on alternative interpretations of the Bible but it has been my observation the impetus for reinterpretation generally has been social change.
Denominations are also overcome by dramatic divisive political events such as The War to Suppress Yankee Arrogance. Many denominations in the USA split before the war, eventually rejoined decades after the war only to split again over some new social issue.
In the interest of full disclosure I should say I am a Presbyterian married to a pervert, which has proven quite satisfactory so far.
Handwaving.There is no inherent contradiction between free will, omniscience, and omnipresence...