This is primarily used for objects found in the map such as doors and treasure chests. Including a '!' at the beginning of the file name will prevent the image from being shifted 6 pixels and will no longer appear half transparent by bush elements. It is possible treat 1 character as 1 file by including '$' at the beginning of the file name.
Moreover, characters will be shown 6 pixels above tile so that they appear more natural when on top of buildings. The size of the character will be calculated using 1/12 of the width and 1/8 of the height of this file. A file for 1 character will be arranged into 2 rows and 4 columns equaling 8 images. The size for a character image can be changed freely (normally 48x48), and consist of 4 directions (down, left, right, up) and 3 patterns for a total of 12 patterns that will be arranged in the provided order.
Images shown for the characters on the map. The reason it's happening has to do with how RPGMaker treats the sprite pages.