A common problem faced by new users to RPG Maker is the transparency. By default all resources distributed with the maker are set up correctly but when new resources are added many make the mistake of saving files directly to their project's materials folder. Without setting the file's transparency, how does your project know which colors to display?

This is what your maps would look like if you haven't set the transparency. You will need to open the materials manager.

This is the material manager icon.

Select the category your file belongs to, then hit import.

Browse to find your file on your computer.

Left click on the background colour. In this example it is white. The transparent colour swatch will turn white.

And now your tileset should look the way it was intended.