Given that the crew decided to re-fuel halfway to their destination, I very much doubt they forgot to raise the gear. More likely is a technical fault requiring the gear to be left down for the transit flight. This could happen for a number of reasons.
A gear left down will consume about 80% more fuel, therefore, and unlike the Dutch 757, one needs to be very careful about fuel consumption and you must not use the FMS for predicting the fuel burn.