Here are things that made me go hmmm.
The lack of activities for the children and teenagers. I didn't see why there couldn't be a nursery for babies and toddlers and something like Sunday school for older children. So many things were way over the heads of kids, even teenagers. It seemed to me the JW experience was at times oppressive to youths. I discouraged my daughter from Baptism because I felt only mature adults should make such decisions and face the possibility of being shunned.
Superstition: the governing body often mentioned other people and their fear of evil spirits or their superstitions. I wondered how their fear of demons was different. I also wondered about their fears that an object could be attached to demons, for example something you picked up at a garage sale or thrift shop.
Babies not being resurrected unless they breathe the breath of lifel
Higher education being frowned on.
Being pressured to quit good jobs with good benefits because they interfered with meeting times or weekend field service.
Lessons about Pharisees, then some articles encouraging JWs to behave like them. JWs behaving like Pharisees.
Uniformity--it seemed as though the governing body aimed to quash any individualism or thing that made a person or family unique.
This was a huge one for me: disfellowshipping mentally ill people.
My nephew was repentant, but was disfellowshipped hastily. An appeal committe was brought in and they backed the first committee. The PO from our congo gave a public "Phewww" after the appeal decision. Both committees were wrong. He had done everything to show his repentance, including putting in 60 hours per month in FS. There was a long delay in his first judicial hearing because there weren't enough elders to make a committee. Meanwhile, he busted his arse showing how repentant
That same PO was hitting on the sisters. Finally one of them, a bipolar, but very sweet pioneer named Yvonne exposed his passes at her, which included him telling her not to take her meds, but to meet with him privately for counseling. He was deleted as an elder and removed as a pioneer. But she was removed, too. His wife said to her, "Why'd you have to open your big mouth?" Yvonne had given him the chance to go to the elders himself. He never did, so the CO forced the issue.
The crushing burden of meeting/study/field service schedule. Jesus said his yoke was kindly and light.
Apostate shake up/witch hunt at bethel and the super hysteria over apostate literature.
Opinion of individual bros becoming local policy, such as pressure for brothers not to wear necklaces or bracelets.
It became more and more clear, that the WTBTS cared more about how they looked to world, but did not care how they appeared to baptized jws and their families. Once you were baptized it was, "Keep your mouth shut or we will kick you out and shun you. We don't care what you're upset about."
Ideas about marriage: husbands making bad decisions about finances or child rearing, etc. The JW model for marriage set up both husbands and wives for disappointment in each other and marriage.
The micro management of the flock and the constant pressure to do more and its affect on both mental and physical health. Also its affect on morale in the congregations.
This isn't an exhaustive list. It isn't in chronological order. The biggest issue was seeing less and less of this love the true organization was supposed to have. Also, their definition of love was very warped.