There are several factors which set up church members for a crisis of faith on some level. Several of these factors are cultural, primarily due to people naively propagating false ideas. For example, evolution is usually stated as against Mormon doctrine and just a theory. In actuality, the Church has no official stance on evolution regardless of what some uniformed individuals have said. Although I can't find my source for this fact, it is accurate with my anecdotal experience that 99% of LDS people with at least a bachelors in a biological field of study consider evolution to be a scientifically proven fact, on par with the theory of gravity and germ theory, and that God used it in some way to create the animal kingdom as we know it. Other examples of false ideas that set us up for failure would require a much lengthier piece to discuss, but would include the whitewashed history of Joseph Smith and polygamy, extent of the fallibility of prophets, the assertion that everything said over the pulpit by a General Authority is doctrine, the generally accepted assumption that doctrine (the broad definition of) never changes, or overlooking the nebulous implementation of the priesthood ban. I'd rather not discuss the details of these for brevity and to keep from inadvertently causing others who are unaware to start a faith crisis of their own before having a sure foundation.
When the contrast between these false ideas and the reality is recognized it creates cognitive dissonance in the believer. Instead of being able to discuss the issues with other members in a healthy way, the Mormon cultural pressure against speaking out on disagreements pushes people to keep these issues swept under the rug. Furthermore, they assume that since nothing is wrong with the perfect church, then something must be wrong with you. When you speak out you are seen as lacking the faith that would make these disparities a non-issue. In reality, it isn't lacking faith, but not choosing to turn a blind eye to the undeniable. One of the most dangerous and common assumptions is that if you don't have a strong enough witness to not be bothered by these issues then it is because you are either sleeping around, breaking the word of wisdom or addicted to porn.
In addition to this culturally based rejection of questions and questioners the Church itself sets up members for a crisis of faith. On the one hand, the Church has "whitewashed" some of its historical warts. Many unpopular facts have been left out of the correlated materials like our Seminary, Institute and Sunday manuals. On the other hand, the Church has encouraged members to do a lot of personal study and get a good education which encourages critical thinking. This is problematic because most of these contradictions are found in our own LDS history books. There isn't even a need to go to anti-Mormon websites to have your faith shaken. I understand how church leadership and members might have encouraged whitewashing in the past in an effort to put the Church's best foot forward, but this won't work anymore in today's environment with the internet and public scrutiny bringing some of these warts to the surface for everyone to see. The Church is starting to correct this with more openness as can be seen with the Joseph Smith Papers project and Elder Marlin K. Jensen's comments about how President Monson wants to help the youth get the history correct the first time around.
This crisis of faith trap becomes most apparent when a person's testimony of the Church is founded on pillars such as an overly perfect view of Joseph Smith or cultural beliefs which contradict science. Learning the truth can take the base out from under their testimony. Then it comes crashing down, although it didn't have to be that way. Sunday school isn't necessarily the place for the discussion of some of these issues. If they were discussed in Seminary or at least spoken of more openly, people could build their testimony on a more sure foundation, one that won't easily be removed later. We know that we should build our testimonies on the core doctrines, but it's too easy to build it on our cultural understanding of Mormonism, including everything from food storage to the Atonement.
Some may say in this situation I should be more faithful like Adam who made an altar despite not knowing why. We should be faithful and do things even if we don't understand why, but that doesn't mean we shouldn't question or try to figure things out. "God himself does not seem to object to our questioning even Him and His ways. Abraham persuaded the Lord to save Sodom if He could find ten righteous souls. Jacob wrestled with his heavenly antagonist until he got his way. And most impressive of all, Job challenged God’s justice and compassion and stood by his own integrity through an extended debate." As Hugh Nibley put it: "I know perfectly well that it is true; there may be things about the Church that I find perfectly appalling—but that has nothing to do with it. I know the gospel is true."
The best way to describe the crash that comes from this crisis of faith is to compare your understanding of life as a Mormon to a solid building. Because Mormonism is all-encompassing, when your testimony crashes, your entire paradigm crashes. To move on you have to rebuild that building. You still have to have a structure that is your understanding of life, who you are, where you want to go and what you want. To do so, you must go through each brick of this broken building, brick by brick, to decide which ones to keep and which ones to throw away. The compounding and traumatizing problem is that your tools of evaluation were also destroyed when the building came crashing down. In this moment, you don't know if you can rely on the scriptures, the words of the prophets or what you understood as the feelings of the spirit. You're starting from scratch without a blue print. Even if you don't go through a complete crisis of faith, once you recognize the problems described is this essay, intellectual honesty requires that you also take a new look at every brick in your building.
For example, imagine the brick of modesty; it can be very hard to decide what guidelines you should follow if some of the counsel could be from humans instead of faxed instructions directly from God. If our body is a temple, should we not respect it and if so how much? If they are sacred temples, should we cover them much more than we do now, more like what the church members did in the 1800's (wrist to ankle)? Why is it fine for men to bear their bellies in swimsuits, but not women? Why does being sacred mean we have to cover it or not let its shape be known? Is modesty just avoiding things that promote sexual desires? Is that why some don't think it is immodest for obese people to wear tight clothes, but it is bad for a fit and large breasted woman to wear tight clothing? Do women need to have shapeless, androgynously clothed bodies? All of these questions are difficult to answer without the tools such as infallible statements from prophets, undeniable guidance from the spirit or cultural practices being universally accepted as God's will.
Once that awareness has occurred, whether it comes with a crash or not, the person has an emotional difficulty dealing with these types of questions on their own. For example, once you are aware that prophets are fallible, how do you know which statements, doctrines and policies are divine and which are human constructs? The only way to know is to get personal confirmations through the spirit. Therefore, your salvation is ultimately between you and God. You can't cheat and just go on what the leaders and culture tell you to do. You actually have to work things out with God making yourself ultimately responsible for what you do. Further emotional difficulty comes from sitting in church meetings and knowing the traditional narrative so oft repeated is not accurate and potentially damaging to others as I've outlined above. You want to speak up to help others avoid the crisis, but it's difficult to deal with the problems that are created when you do.