I can only tell you my personal journey
First, it was the hypocrisy I saw in Christians. They would condemn in others what they themselves were guilty of doing. They would talk about charity and peace yet be greedy and violent. And, often those loudest about their Christianity were those guilty of the least "Christian" acts.
Next, it was the inconsistency of the Bible and the doctrine. Different clergy and different denominations saying different things, yet all of them claiming they were drawing from the Bible. The claims that the Bible is 'true' even when it clearly wasn't. The lies told about science in the name of pretending that the Bible was accurate.
Finally, I recognized that all religions are on shaky ground philosophically. There just is no evidence for God, and what arguments can be made are the same for all religions, and yet those different religions claim their doctrine is correct and others are wrong.
