It will depend upon the context. Do you have a link to the documentation you are referring to?
In the context of a Windows Azure Virtual Machine the phrase VM Instance does refer to the ability to create a Virtual Machine either from the gallery or from the ground up.
In the context of a Cloud Service (the PaaS model) both the phrase VM Role and VM Instance apply. The VM Role in this context is a definition of a virtual machine that will run a specific set of code. For example, you might have a VM Role defined that processes orders or one that computes number crunching algorithms. This is a template if you will, or a role that defined for your application. When you define a role you also indicate the number of instances of that role. So in the context of a Cloud Service the VM Instance is a Virtual Machine that is running the code defined for the role it belongs to, but there might be ten more running the exact same code.