This message is not proof that something is really broken, it only indicates that there might be a problem because the request in question runs for so long. Ivy issues this message for all long-running requests. For external requests (users via browser or web service requests), this message is issued after 5 minutes, for system requests, the threshold is one hour. The endless loop checker job runs every 5 minutes.
It may well be that all is in good order, but Ivy cannot determine this.
A good example to illustrate this behavior is a long-running import of data: A single REST call retrieves several gigabytes of data. It runs for several hours each night. It gets one of these messages logged every five minutes after the first hour because it runs as a system request, even though all is OK.