Also make sure you don't place on your map any tiles with index above 253 (I believe, or very similar). You can have more tiles in your tileset(s), but anything above 253 should be a death tile (used when you destroy some other tile).
Not 100% sure about 253, maybe it's 252 or even 254.
If you ignore this rule, your map will be saved, but won't work correctly in the game - the problematic tiles will disappear.