For me, there's a few.
In Super Mario World, for some reason I didn't figure out that picture on a dragon coin was a yoshi head until just a few years ago lol. Instead, for some reason, I always saw it like a mitten, holding an upside down spoon, like so.
Another one was Mario's death GFX. For some reason, I always viewed his hat as his upper lip, and the red area inbetween his nose and hat, as the inside of his mouth. So it bassicly looked like he had his mouth open REALLY wide, like he was crying like a baby, which was what i assumed lol.
Oh, and I made what I think might've been the common mistake, of thinking Mario's mustache was a smile. Oh and I thought Mario was Mexican. I couldn't have been the only one... right? lol. In SMB3 for GB, when he says "Let'sa go!", it sounds like "Mexico!"
So what about you guys? Is there anything you grew up seeing the wrong way?