Ah ha. I ran into that bug the other day for the first time but didn't know what caused it. I'll fix that ASAP. Thanks. (Edit: It's now fixed)
Currently there's no way to save. I consider the game to be a rogue-like in that sense. The idea is that the game should last 30-45 mins with permadeath. You either escape or die trying. I am considering putting some limited save points in though, like immediately prior to each boss fight, but if you continue the save will be deleted. You have one chance.
I'm sure some save points will be required when I add more bosses. At that point a playthrough could take 2+ hours and offering a save point before each boss is probably the way I'll go.