I know that this kind of stuff could happen before. Node.js is still a recent language and some really nice features like the cluster module had to evolve and PM2 also.
Now, for instance, the hot code reload (that is called reload now) has been re factored to provide a strong production ready feature. But you need to know that you have to use Node.js 0.11.x to use the "cluster_mode". A reminder has been added to notify the user about it.
So things evolves, and I hope in the right direction!