Gods, I don't even think I can list all the things that made me think twice about the JWs.
Not sure if this is specifically a JW belief or not, but the concept of the number 7 representing perfection (I've never heard anyone say "That was a perfect 7!")
The supposed nonexistence of a a zero year - maybe it's because I'm a creative person, but I don't see what's so illogical about it
That a person must be a faithful JW in order to be saved (very elitist IMO); actually, the whole concept of salvation while other human beings get destroyed doesn't sit well with me
How a person "knows" that they're one of the 144,000 (never got a satisfactory answer to this)
Women being viewed as "the weaker vessel"
Homosexuality being a "perversion"
Having to "do more" when one's plate is already full of endless meetings, hours of field service, study, etc.
Not being able to let your hair down on vacations (it's not a vacation unless you can do that!)
And I especially love Finally-Free's observation that "Thousands of years of suffering in the world takes place because Adam and Eve ate some lousy fruit that didn't belong to them." LOL