I have been playing around with the level editor and it looks sweet!
Here are a few other lil things I have spotted up to now that I haven't seen mentioned here in no particular order...
1. When you want to start over and hit 'new' it doesn't seem to delete the animal sprites that have been previously placed in the scene.
2. When you click the menu at the bottom (layer numbers, etc.) it is easy to accidentally place the current tile/prop/object in the scene somewhere behind the black border without realising.
Maybe make the whole black menu background area at the bottom into a pickable quad (like a large button with no functions attached), so if the mouse hits any buttons or this black bg border area nothing is placed in the scene behind it.
3. When you make a tile selection and it draws the grid, it would be nice to de-select and remove the grid when you press the delete key, as the selection is no longer needed when the tiles are removed.
Keep up the good work, hope this helps!