One of the first things I would try, at least as a temporary fix to this problem, is to increase slightly the distance that a character has to fall before taking damage. The way the bug seems to work is it thinks that the character is falling a small enough distance that he doesn't immediately take lethal damage. Instead, the character takes damage repeatedly over and over, as if falling several times in a row. I'm sure there are other things that you can try to address the issue more directly, but at least this will make the game playable in alpha in the meantime.
May 11 2016
May 10 2016
Confirmed, and still happening on 0.49 stable.
Confirmed that this has happened to me several times in 0.49 stable. The tell-tale sign is ruined pants and boots, broken legs, and no gunshots or players anywhere nearby. Usually the first "fall" doesn't kill me, but usually what happens is it thinks I fall many times over a very short period, and sometimes it's enough to outright kill me, other times it just breaks my legs and ruins my pants and boots.
Is there any word from the devs that they are actively working on a solution to this bug, or are they only aware of it without knowing how to fix it? I really want to know when it comes to this one in particular, as it ranks #1 on my list of bugs that completely ruin gameplay, because there is absolutely no way to avoid it other than never going on the second floor of buildings.
I have two things to add regarding this since the 0.49 update.
I have personally lost 2 AK's that I've dropped on the ground when outside a building. One I dropped on the road, so I really doubt that I "missed" where I dropped it. Both times I was running while it happened, because I had to drop it to fight a zombie.
Another thing related to this is I found a bandana: camo pattern on the second floor of a green house. My inventory was full, so I proceeded to untie the bandana, then tie it into a face mask while it was still on the ground, so I could wear it on my face. When I untied the bandana cap into a bandana, it worked fine, but when I tied the bandana into a face mask, it disappeared. I scanned the whole house, both floors, as well as the outside of the house very thoroughly, and it was nowhere to be found. I also logged out and back in after removing one of my inventory items to see if it would appear in my inventory, but it did not.