In the short documentary that's part of the Michel Gondry music video collection, he says that when he was a child, he lived on the edge of a city, and always wondered if the earth was a solid ball of city with a splotch of countryside on it, or a solid ball of city with a splotch of city on it. This is one of the more whimsical childhood misconceptions I've heard, but I think everyone had at least a couple.
My dad said, for example, that when he was a kid growing up in Hartford, he was always confused why the state of Connecticut was sometimes shown with its little appendage on the bottom left, and sometimes with it on the top right. The version with it on the top right, he later realized, was the United States.
Likewise, for me, in the apartment building where my grandparents lived, there was a set of emergency lights mounted on the wall next to the door of the neighboring apartment. One time I asked what they were for, and the response got scrambled enough in my young brain that for quite some time after that I was under the impression that there were emergency personnel (EMTs, firefighters, etc.) who waited in that apartment until they were needed to respond to incidents.
I would enjoy hearing about any other childhood misconceptions in the comments, if you're willing to share.