That usually happens to me when I let it rise too long. It also will happen if your house is very warm, because then it rises more quickly in a shorter time. Try a twelve hour rise and see if that fixes it.
You also might want to try the Cook's Illustrated version of the recipe, which they claim is more reliable:
Almost No-Knead Bread, Cook’s Illustrated
2 cups unbleached all-purpose flour (10 ounces), plus additional for dusting work surface
1 cup whole wheat flour (5 ounces)
1/4 teaspoon instant or rapid-rise yeast
1 1/2 teaspoons table salt
2 tablespoons honey
3/4 cup plus 2 tablespoons water (7 ounces), at room temperature
1/4 cup plus 2 tablespoons mild-flavored lager (3 ounces)
1 tablespoon white vinegar
Instructions
1. Whisk flours, yeast, and salt in large bowl. Stir honey into water, then add water, beer, and vinegar to the dry ingredients. Using rubber spatula, fold mixture, scraping up dry flour from bottom of bowl until shaggy ball forms. Cover bowl with plastic wrap and let sit at room temperature for 8 to 18 hours.
2. Lay 12- by 18-inch sheet of parchment paper inside 10-inch skillet and spray with nonstick cooking spray. Transfer dough to lightly floured work surface and knead 10 to 15 times. Shape dough into ball by pulling edges into middle. Transfer dough, seam-side down, to parchment-lined skillet and spray surface of dough with nonstick cooking spray. Cover loosely with plastic wrap and let rise at room temperature until dough has doubled in size and does not readily spring back when poked with finger.
3. About 30 minutes before baking, adjust oven rack to lowest position, place 6- to 8-quart heavy-bottomed Dutch oven (with lid) on rack, and heat oven to 500 degrees. Lightly flour top of dough. Pick up dough by lifting parchment overhang and lower into pot (let any excess parchment hang over pot edge). Cover pot and place in oven.
(I think they found that not flipping the bread resulted in a more reliable rise in the oven. I have never found the flip to be the problem, though.)
Take heart!! Take a break, and then take heart! You can do it.
