That is a little early for bunnies to be leaving the nest box, but by 12 days old they are at least well-furred and have each other to help stay warm. And honestly, 42F isn't all that cold; it's not so warm that they should be leaving the box to cool down, but they'll probably be just fine if they hang together. Unless there's something very wrong, kits more than a few days old seem to know what to do to keep themselves comfortable.
As for why they all sometimes want to be in the front of the box, I haven't entirely figured that out. Your instinct to clean out the box was good - it was what I would have suggested first. Once in a while there's a dead bunny left undetected under the bedding, and the living ones, if they can't push it out, will sometimes do what they can to get away from it once it gets, uh, ripe. The other thing that can happen, if the box or cage is tipped slightly toward the front, is that gravity sort of prompts the bunnies to gather at the low point. I've started to build my nest boxes with a floor sloped toward the back to prevent that.
A common reason bunnies pop out is, as you observed, that they're hungry. Since 12 days is a bit young for kits to be eating a lot of solid food, you might think about giving the doe a little extra fat in the form of BOSS or oats or Calf Manna, to help her produce more milk. It doesn't need to be a lot - a tablespoon should do. Has she noticeably lost condition in the last two weeks? It's a good idea to weigh your does 1-2x a week to catch weight loss, since once they are obviously skinny they've really gone downhill.
As long as they're not crying, I wouldn't worry about the kits getting stepped on by the doe. They're pretty sturdy. 
