1) Are goblins supposed to be able to hit targets behind fortifications?
Yes; fortifications aren't perfect defenses. When a shot would pass through a fortification that the shooter isn't adjacent to, they must make a skill check. If successful, the shot goes through, otherwise it bounces off the wall. Of course, higher skill levels allows for passing the skill check more often, thus fortifications are less effective against highly-skilled enemies.
2) If so how often does it happen?
As implied above, it happens much more often for elite marksgoblins than the run-of-the-mill ones that come in swarms. It's almost to the point where normal marksgoblins are totally ineffective against fortifications, and fortifications are totally ineffective against elites. Another part of the problem is that elites get a higher rate of fire, so even if only half of their shots go through it's still like the defender is sitting in the open against a few normal marksgoblins, which is of course very much lethal if unprotected.
I seem to remember hearing that the skill check's difficulty is dependent on how far away the shooter is from the fortification (where horizontal distance is exactly as beneficial as vertical distance), but I might be wrong. If so, putting a wide moat around your tower, or even just a ring of wall grates or bars a distance away (grates/bars don't interfere with ranged attacks at all, so they're good for surface shooting galleries where moats are impractical), would help protect your defenders further.
Basically I want to know if this is a bug or I'm just super-unlucky.
Nick
You might just be super-unlucky, but probably not. In the future, armor your marksdwarves, give them wrestling training when possible (for the dodge% boost), and have them carry shields. Marksdwarf defenders are rediculously effective, but they're not invincible.
How far can something fall and still live most of the time? I want to make a pit to toss enemies into that has a dragon at the bottom. I want them to live long enough to fight the dragon. I want them broken but not dead.
5 is often fatal, but in my experience isn't often immediately fatal (they land, then bleed out). If you want them to actually "fight" the dragon, 2-4 should be enough to give them bruises and broken bones.