I swallowed a lot of what we were told. But.......
I've always been interested in science, and I had trouble accepting that the dating methods (carbon-dating, etc.) used by science could be THAT off. I mean, they find tools obviously used by something other than animals that are 40,000 years old (pulled that number out of my bum; I'm sure there are much older ones), but we're supposed to believe that man has only been on the earth for some 6000 years. That niggled away at me.
I had trouble with the dinosaurs. I mean, why would God create them only to destroy (or let them be destroyed) them long before man arrived? What was their purpose? I was talking about that with another JW once, and they said, "Maybe God didn't realise how big they were going to get, and so he had to destroy them." That made me even more confused, because how would God not know what was going to happen. "Oops! I didn't know they'd get THAT big. Better kill 'em."
I too had trouble with the "no rain before the flood" thing. I mean, come on, all the tropical plants (clearly seen in the fossil record) survived because of some dew every morning?! Must have been some friggin' heavy dew...in which case, why not call it rain?
I wasn't too sure about the 1918/1919 thing, mostly because I just didn't understand how they got it.
I too wondered about children being destroyed at Armageddon. Most JWs in my area just said that God could read hearts and knew how people would turn out, so he would save those who deserved it.
I was beginning to wonder how the GB actually got their info from God. I wondered about the "mechanics" of the whole thing, considering that I thought the Bible said that God didn't speak to men anymore.
Once I started really thinking about my doubts, they grew stronger.