Why does my bread rise unevenly or from the bottom in the oven?
For the first bake, that didn't form a bottom crust - it sounds like the bread stone might not have been heated enough.  An oven with a baking stone needs a lot more preheating, since the reason the stone is useful is that retains heat; it's as slow to cool down as it is to heat up.  If the stone was still absorbing heat when you put the dough on, it would keep the bottom from baking properly, since the temperature would be cooler.  Try preheating your oven about a half hour more before baking, next time.

For the uneven rising, I'm not sure - it seems like your dough wasn't finished rising before the top of the loaf had already started setting, and it expanded wherever it could.  If the top surface of your loaf got a little dried out in your last rising before baking, that stiffness might encourage the rising dough to expand where the dough was softer and still moist.  You might brushing the dough lightly with oil during the last rise, or with water just before baking, to keep it flexible enough to rise evenly.  

If your dough has a moist surface, the problem might be that it is under proofed (mentioned in the comments here), and needs to rise a little longer before being baked - It will rise in the oven a little bit anyway, but if it has extra rising potential because the yeast wasn't finished, it keeps trying to rise during the baking time, and once the top starts setting it will expand wherever it can.  There are ways to test the proofing, one I saw was to poke the bread, and if it springs back quickly it is under proofed, slowly and it is ready to bake, and if it doesn't spring back it's over proofed.