Running instances is a tricky one to solve as it can have many causes, infinite loops, incorrectly handled exceptions, etc.
First thing I'd recommend is to check your Host Server log files: Make sure error logging is enabled and check if there are any useful entries logged. Which version of K2 do you have installed?
Also, if this is a production environment, I would also encourage you to open an official support ticket, if you can't delete instances from Workspace, something is definitely knocking under the hood.
Thanks for the help dc.
It ended up being a call to a web service, which first times out but if more processes hits it, it stop timing out and then k2 just keeps on running.
I fixed this by renaming the web service and then restarting the k2 service. This results in the processes going into error state rather than running state.
At least with it being in error state, the workspace worked again and I could look at the reports to see where my process broke.