The first doubts I had were about the bible itself. The flood story was too outrageous for me, even as a kid. And the cruel and unjust way god seemed to dispense punishment in the Old Testament. The story of David and Bath-Sheba's child never sat well with me. I could never get a satisfying answer as to why the child needed to die.
As far as JWs go, the biggest issue for me, initially, was the idea that they focused so much attention on their works, yet at the same time promoting the idea that salvation was a free gift, not something we could earn. I could never reconcile this contradiction. I never believed we were being genuine when we said we were being motivated by love. I decided that I wasn't going to waste any more of my life if I wasn't convinced it was the truth. That led me to investigate the religion further, from outside sources. Now I don't believe any of it, anymore.