Nano-Bots can only be destroyed when their mouths are open which can occasionally side track you and compromise your ability to steer your critter around the terrain of each level. Therefore it is safer to avoid the Nano-Bots altogether rather than destroying them.
During the game, try keeping your critter as close to the center of the screen as possible otherwise you could end up getting too close to the edge where a fiddly tap could send your critter to it's death.