1.) Check that all your tile dimensions match up
First, make sure when you import the tile image sheet into Stencyl that you set the dimensions accordingly. Then, when you create a new scene, make sure the scene tile dimensions match what you put in for the tileset! The tiles might display somewhat correctly in the editor, but probably won’t when you actually test. The latter detail with scene tile dimensions is a bit easier to glaze over, so make sure you do it for every scene you create!
2.) Make sure you selected the transparency colorkey
In other words, when you import an image, you typically have some background color (sometimes white but often another color). You need to click this background color on the image so Stencyl will “remove” it in game and make that area transparent (the help text should tell you do so as well). Make sure though that the color is something different than what is used on the actual image. A common mistake is to use white or black as the colorkey, but often white or black is used somewhere on the image in question. ALL of the color you select will be removed, so be aware of that.
3.) Make sure you have set up layers correctly in scene
Sometimes when you set down a tile on top of another, it disappears. That’s because a layer can only have one tile at any given point. In the scene editor, look to the bottom-right to see the layer commands and management. You can add layers, where layers at the top of the list display their tiles on top of everything else and those on the bottom display their tiles below everything else. In other words, a layer’s tiles (or actors) can still be there but layers on top get precedence when displaying. So if you need to do something like place a house on top of grass, make a lower layer with grass tiles and a higher layer with the house tiles. Note that layers do not typically affect collisions; two actors on two different layers can collide with each other.
4.) Make sure your window isn’t bigger than the scene
In game settings, you set the size of the game window. If your scene is smaller than that window, there will be blank space on the bottom or to the right of the window. Make sure the scene is at least the same size or bigger than the actual game viewing window.