Pilots may preflight the load, but they can't catch all the defects. The pilot's preflight is only a last-minute check of the obvious. It is the loadmaster's responsibility to ensure all the technical aspects of the load are complete.
It is extremely unlikely that the flaps were retracted instead of the gear. Besides being WAY out of the habit pattern, the FLAPS 1 gate makes it damnear impossible to select the flaps UP inadvertently.