Is there any way of preventing this from happening? I use microsoft paint (windows 8 version and I recolored a sprite, but when I open the file again, it mixes the 1x1 and the 2x2 pixels together. Can anybody tell me how to fix this problem?
You sure need to get a different Paint Program that you can save on .GIF Files without having to get some random 1x1 Pixels in your graphic. Get Paint.NET for example because that program is in my opinion easy to handle once you get used to it.