When you say that they stopped, what exactly do you mean? Was the instance gone? Was it in the Busy state? What was the exact message in the portal? How did you recover them?
I suspect when you say stopped you mean the VMs were rebooted unexpectedly and then came back online shortly after that. If this is the scenario, check out http://blogs.msdn.com/b/kwill/archive/2012/09/19/role-instance-restarts-due-to-os-upgrades.aspx for information about OS updates in Azure and what you would see in your roles.