It's often just something like a dream, non-canon story, or a trick intended to teach Lois Lane not to be so uppity. But sometimes the covers just flat-out lie. There's one where the cover shows Superman standing in front of a flowing fire hydrant, cheerfully announcing to a crowd of people dying of thirst that none of them were allowed to drink it. The actual story inside has completely the opposite scenario, where some supernatural force has driven the citizens of Metropolis to avoid water and Superman is flying around trying to get people to drink.
I sort of wonder if these comics were written like the old sci-fi rags, where the cover was drawn first and the editors just paid one of the staff writers to make a story around it.