My guess is that the game is spawning the atoms by normal distribution. The changes for higher and lower atom spawning is statistically low but present.

UPDATE

I've found the exact logic behind atom spawning in the [developer's own introduction page][1]. The 3. and 4. rules control the behaviour that you're observing.

> What are the spawning criterias?  

> 1. You get a plus at least every 5 moves.  

> 2. You get a minus every 20 moves.  

> 3. Every 40 moves the range of possible atoms increases.  

> 4. If you have atoms below this range in the circle they can still spawn with a chance of 1/(Amount of atoms in circle).
  
> 5. Neutrinos spawn with a chance 1/60 when the score is above 1500.  

> 6. Dark pluses spawn with a chance 1/90 when the score is above 750.


  [1]: http://sirnic.com/atomas/