Runner's fractures in the fore-foot were something that came up when I was researching running with toe-shoes. You're definitely right that it's a risk. I've heard of it mostly happening when people don't ramp up slowly, as bones, like muscles, become stronger when you use them [1].

Switching to Vibrams and then running further and harder than usual may well cause stress fractures, though I think that has to do with the changeover from cushioned shoes, not intrinsic to the shoe or running style -- it's common for many folks in Latin America and Africa to run barefoot by default without higher incidence of fractures.

[1] http://www.nichd.nih.gov/health/topics/bonehealth/conditioni...