This is a great topic, though at the moment, I am having difficulty recalling my childish misconceptions, though I must have had as many of them as anyone else. Here are just two:
Stephen Jay Gould, a second-generation American, somewhere recounts the shock that he experienced when he first met some people who were grandparents yet spoke without a foreign accent. I recall experiencing the same perplexity, though I don't recall how old I was at the time.
About human reproduction, I remember reading an illustrated book for children that explained conception, pregnancy, and birth, but it gave me no clue as to how the sperm from the daddy got into the body of the mommy. I assumed that it was something that happened in consequence of the marriage ceremony. Then I saw an episode of a television series set in 19th-century America in which there is a big scandal about a woman who arrives in town who has a child but no husband and is not a widow. My theory was overthrown, and I had no idea what could explain how a woman without a husband could bear a child.