Plot hole: Throughout the entire movie, barns, houses, cars, 18-wheelers, etc. are demolished and lifted into the air like they were made of paper. And yet Jo and Bill pass through one tornado after another with nothing more than their hair getting messed up a little. You'd think the debris alone flying into their faces at 100 miles an hour would be enough to give them a few injuries.
Plot hole: During the scene when Jo introduced the first Dorothy to Bill for the first time, you can see the blurry figure of Dusty and Dr Melissa holding hands in the background, which is super weird given she was annoyed by his presence at that point.