Even if a child has never had a bad encounter with short men, simply by viewing something like Shrek with its nasty portrayal of Lord Farquaad's Napoleon Complex, that negative idea will always subconsciously be in the back of their mind. This will rear its head as confirmation bias later, once they're older and run into any short man they dislike, or they simply feel like discriminating and need justification to do so.
Inb4 every adult suddenly has an anecdote about how a short man abused them as a kid, which proves short men are evil (something people would never dare claim about any other genetic trait).