A skeleton was shooting me, but two meters above me. I shoot through the waterfall and killed it. The skeleton was missing because was shooting over the water blocks.
Environment
Windows XP SP3 (because Minecraft doesn't appears to work well on Ubuntu)
Java Version 7 Update 9
Unable to reproduce in 1.4.5. Skeleton is shooting and hitting me when swimming above me and I'm underwater and if I create a waterfall, the skeleton is still able to hit me.