How about making it possible to flip some tiles in the wrong layer, if they contain enough of that layer's colour, that they could conceivably belong to it, thus making it impossible to satisfy clues in the other layers if you make a mistake?
Of course the simplest solution could just be to turn off the "painting" mechanic altogether. Make each tile require an individual click, and it would be a lot less rewarding to click aimlessly.
Incidentally I noticed that it sometimes takes a while for the game to notice that a clue is solvable, and enable the relevant tiles. I didn't understand what was happening the first time I played it, and thought it was just my touch-screen playing up, but for example after you mark the X's that make the 2 clue in the top row solvable, you can't immediately flip the remaining two tiles, but have to wait a few seconds before you'll be able to flip them.
-Neelix