The toughest one for me was one I attended where the doctrine was sound but there was no grace. None. I was so focused on the teaching (which was correct, straight from the bible, verbatim) that I missed the part where people were getting hurt because they (and their children and spouses) were expected to be "perfect" (for lack of a better word). Individuals ran the risk of being "disciplined out of the church" for unbiblical behavior. I suppose it was more legalistic (like raising little Pharisees) than Christ like. Every little thing was pointed out and immediate correction strongly encouraged. It was brought to my attention my children did not sit quietly during service with their little hands folded in their lap, listening to the pastor. They fidgeted, whispered, drew, colored, did not stand up during singing, etc. It was not until I was no longer attending that I saw how judgmental and ridged I had also become, myself.
The second most challenging one was a chain of "churches", located all across the nation. I would seek them out each time I was on a trip. They were wonderful, truly! But corruption, at the highest level, came to light and that ended that.
Now, the place that caused the greatest discomfort in me was one where man was praised but it was so subtle at times, I had to pay very close attention to grasp it. Further, sound doctrine was mixed with false doctrine in such a way it all sounded correct at first...but there was a nagging (perhaps by the Holy Spirit) that something was not quite right. For example, during a message the pastor stated, "Our faith is living and active, sharper than any two-edged sword, piercing to the division of soul and of spirit, of joints and of marrow." Did you catch that?! The TRUE verse is,
For the word of God is living and active, sharper than any two-edged sword, piercing to the division of soul and of spirit, of joints and of marrow, and discerning the thoughts and intentions of the heart. And no creature is hidden from his sight, but all are naked and exposed to the eyes of him to whom we must give account. (Hebrews 4:12, 13 ESV)
He replaced THE WORD OF GOD with "our faith" hence taking glory from God and giving it to man! This is exactly why I feel memorizing scripture is important...not only to be able to retrieve it when needed but also to recognize when it has been changed!
Put on the whole armor of God, that you may be able to stand against the schemes of the devil. Therefore take up the whole armor of God, that you may be able to withstand in the evil day, and having done all, to stand firm. Stand therefore, having fastened on the belt of truth, and having put on the breastplate of righteousness, and, as shoes for your feet, having put on the readiness given by the gospel of peace. In all circumstances take up the shield of faith, with which you can extinguish all the flaming darts of the evil one; and take the helmet of salvation, and the sword of the Spirit, which is the word of God, (Ephesians 6:11, 13-17 ESV)