It is known that trade by ship is a cheaper way than airway, land, and rail trade. One of the most important reasons for this is that ships use heavy fuel oil (HFO), which is cheap but also poor quality fuel. This HFO used in ships needs to be cleaned with machines called separators (purifiers). Therefore, the separator is one of the vital auxiliary machines on the ship. A satisfactory separation should be done in order to get rid of the effects such as water in the fuel, sludge formation, pump ability, mixing of different grades in the tanks, abrasion, and corrosion, which are the most important risks in the burning of fuel oil. Many problems are encountered while trying to make good separation. Therefore, in this article, 20 important problems that are frequently encountered in ship HFO separators are evaluated with the best-worst method (BWM) by consulting marine experts. Results show that dirty separator discs (also fractured or broken), wrong gravity disc choice (or bad interface position), and unsatisfactory bowl work are the most important problems among 20 critical and frequent separator problems. Problems and results are very important in terms of smooth ship machinery operations and we think that this study will close this gap in the literature by ordering and identifying problems and also solution recommendations.