This just happened to me.
The exact circumstances - had a max AP soldier equipped with a precision rifle, he had clear LOS to the alien (the humanoid one, not the lizard one). The percentage given was 0%, but I fired anyways. The bullet heads right for the alien, then crashes right before it hits. There was a wire fence between the alien and the soldier, but this has never been a problem in the past.
This is using the Desura standard pre-order version, V.12 I believe.