Yes...I have seen that many times. At the end of a test the controller tries to collect data from the agents to merge the results into a single file. If it runs into network problems, or if the agent machine isn't responding for one reason or another you will get that error. You will need to manually get the data from the agent machine and copy it to the controller box in the appropriate sub-directory for that load test and then use the remerge feature in Performance Explorer to merge the results.
It sounds like that machine is getting busy and the controller is failing to be able to communicate with it. Might be that the controller machine is too busy or the agent machine is. Also could be the network inbetween like a hub or a router that has become too busy.