Do you mean the webgisdr temp files? I recall an Esri rep mentioning that was intentionally unintentional. They assumed that if you ran webgisdr once, you would then do so on a regular basis. As a result, the temp backup files would accumulate until the service was called again. This would only happen if you manually ran webgisdr once, and I don't think you can stop it after that point (not that setting up webgisdr as a service is that hard, which is probably the better solution anyways).
Assuming we are talking about those webgisdr temp files, and your webgisdr service is set to run regularly, you shouldn't see those temp files accumulating beyond the scheduled interval.
