Operational delays are delays caused by operational difficulties. It means that crew and/or aircraft are out-of-sync usually caused by late in-bounds, crew illnesses, crew timeouts, etc...

Essentially all delays are operational delays, but when an airline calls it operational it usually means something other than mechanical problems, weather or ATC delays and in most cases it means a crew shortage (pilot called in sick, need to find a new one). But it could also be a result of a broken down luggage belt loader thus causing a problem with getting the luggage loaded on the plane as an example. Because of the labeling as "operational" it isn't often clear to the telephone agents what is happening with the flight.