Churches can be controversial & experience schism just like many places, & the effect of things that may have happened years ago can remain years & years down the track. In this respect the Old Testament church (The nation of Israel) mirrors the New Testament church.
Leaders get it wrong, members have disagreements, and people try & hide stuff & think they can fool God. This is not a testament to the failings of God but a declaration of words & actions that humanity really does have a fallen nature & people can be so unwilling to trust God and His ways.
It is a messy picture & it is where God chooses to confront sin with warning, judgement & mercy. We delight in our long suffering & patient God & give Him praise out of thankfulness for the good & great things He has done.
In this era of anything becomes everything & anything goes (pretty much), God continues to cultivate his church over time. The big & the small, the significant & insignificant are all attended to as believers live by faith & not by sight. Rom 11:18-20.