I had the same issue several times. It seems that Kibana is running with node.exe.
If you look in your Kibana folder (mine is kibana-5.0.0-windows-x86) you can see a folder called node.
If you try to delete the whole Kibana folder, there are some files locked by node, node.exe itself as well.
I used this c# class FileUtil (https://stackoverflow.com/a/20623311/1311130) to find the process and then delete it:
class Program
{
static void Main(string[] args)
{
const string fileLocked = @"E:\kibana-5.0.0-windows-x86\node\node.exe";
var processes = FileUtil.WhoIsLocking(fileLocked);
processes.ForEach(p => p.Kill());
}
}
Honestly I think is awful all this hassle to stop a program running, but until a better solution, this is the only one I found out.