What do those enemy images actually look like? The icons should be automatically placed based on the size of the image, so that looks like you have that much empty space over their heads in the image file itself.
If not...make sure all of your Yanfly plugins are in the correct order according to the Yanfly Engine Web site.
If all of that pans out...well, I still think something is wrong, because they should automatically be placed
But there are notetags in one of the Yanfly plugins to manually adjust the anchor and height and such of a specific enemy...I think they're in the Battle Core, off the top of my head.