It's just that the studio doing the animation did not pay that much attention to these details. If you are meticulous enough, you will discover deficiencies like this in many anime. It's in fact a common pitfall for animation studios.
There are also deficiencies in anime other than height. For example, the location of the mouth is also widely criticized. As you can see in the scene below from Sora no Method, the girl's mouth is totally on the left-hand side of her face, which would be considered as abnormal in real life.