I made pizza dough from this recipe: http://smittenkitchen.com...
and used half whole wheat flour.
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I can see two possible reasons...
1) the recipe calls for "active dry yeast", and then proceeds to tell you to mix it in with the dry ingredients. I find this a flawed step. Active Dry Yeast needs to be activated by mixing in warm water and a pinch of sugar, and allowed to sit for about 5 minutes until frothy PRIOR to adding it to any dry ingredients. If you were to use Instant Yeast (AKA Rapid rise yeast), you can add it directly to the flour with no problems.
2) I also wouldn't mix with 50% whole wheat. I personally would opt for a lower percentage. The rough bran and heaviness of the flour make it harder to get a good rise. It requires extra kneading and a little more moisture since wheat flour absorbs more liquid. I would use 30%-40% wheat flour.
you may need to start over with your dough, or roll it out thin for a crispy thin crust rather than a soft, thick, doughy one.