I think the biggest issue is security. It is so easy to clone a virtual machine it can be hard to keep track of what machines are still needed and which ones arent. We have tried to stay on top of it and are looking at some vendors who offer solutions to keep track of it all.
The biggest impact it has had is in terms of forcing an all new territory battle 🙂
Apart from that, managing the growth isnt easy if there are no defined directives. So that is essential, basically, anyone should be able to point to a policy doc and say, yes, you can create a new vm, or no, you cannot.