The problem here is most likely because of the node graph itself. Say you have 100 sprites as children of the scene, with not sub-children of their own, and they all use textures from the same atlas and default blend modes, then Sprite Kit will batch-draw these 100 sprites in a single draw call.
However if these tile sprites have children of their own, perhaps shape or label nodes for debugging, then this will "interrupt" the batch drawing operation.
Check your node graph. Make sure all tile sprites are children of the same parent, and have no children of their own, use the same blend modes and textures from the same atlas. Then batch drawing will definitely work.
If that doesn't work, verify that the tiles.atlas folder is correctly converted to a texture atlas in the bundle. If you open the compiled app bundle you should find a folder named 'tiles.atlasc' with a plist and one or more png files in it, containing all individual images of the folder. Furthermore none of these individual images should appear in the bundle - if they are added to the bundle as individual files using the same names as in the atlas, then Sprite Kit will default to loading the individual image files rather than obtaining them from the texture atlas.