Moral dilemmas and temptations, duty and responsibility, losing an advantage, miscellaneous challenges

The character finding out about deceptive practices at their place of worship
The character hearing arguments against their religious beliefs that make them question their validity
The character reaching a point in their maturity and growth where they begin to question what 
they've always been taught
Being cast out of a religious community for a transgression
Discovering ulterior motives or unforgivable flaws in a mentor
Seeing suffering in the world that can't be explained away
Struggling with a seemingly insurmountable addiction
Praying diligently for something that doesn't come to pass 
A loved one dying unexpectedly
Being presented with a religious ideal that doesn't fit the character's belief system
Questioning inconsistencies in religious teachings in which certain ones have been discarded while others are held as absolute fact 
Developing a terminal illness that steals all hope
Being the victim of a violent crime
Experiencing multiple miscarriages
The character's marriage falling apart, despite their best efforts
Experiencing progressive traumas, one after the other

Asking questions but being shut down
Arguing with family members and friends who still embrace their faith
The character being judged by their religious community 
Being pressured by others to make a certain decision about their faith
Slipping into negative behaviors to cope with the difficulties that caused the crisis 
Having to reevaluate what's important and what should take priority
Looking for answers and struggling to find an unbiased source of information