The thread title is Fuel in transmission oil? I assume you had the 25 hour or 50 hour inspection completed on a new boat ?
Or is that a miss print and it is a 250 hour service? I'm not sure of which sample had fuel detected in it.
If it was the transmission that showed % of fuel there would be no way that I can think of that fuel would be present unless the sample was contaminated. Many times when a service technician is doing a seasonal or hourly specified engine service he/she uses the same oil extracting device and recovery bucket. Then takes samples from this same recovery bucket. If the technician does not do a full cleaning of the oil extractor and bucket there can be contamination from a previous source. Many times the technicians will change fuel filters at the same time as doing oil and transmission oil changes. Some of the fuel is also disposed of in the recovery bucket. When the oil samples are sent out there are now traces of cross contamination anti freeze, fuel, metal, water,...... In other words the report is incorrect.
In the case that the technician was careful in providing a clean uncompromised oil sample and fuel was present in the transmission I would be puzzled as you are.
If the Fuel was found in the engine oil and the sample was uncompromised Mikes examples would be good reasons for the fuel % present to be elevated. If a diesel is started up at the dock and left to idle for a while and then shut down or idled for long periods of time the engine may not get up to operating temperature. The diesels (even common rail) tend to run rich at start up and some of the unburned fuel can wash the cylinder walls leaking past the rings. This can happen even in a engine with little wear. Unfortunately this engine with little or no wear may have increased wear if this practice continues to happen. The fuel is washing the cylinders of the lubrication film that is present to reduce wear. The oil sampling is telling the engine operator that there is fuel present. It's time to find out where it is coming from to prevent the next oil sample coming back with high % of fuel and high levels of metal particulate. Now there is wear.
If this is your first sample to be sent out and you are not sure of the conditions of the sample. I would not put a great deal of stock in this report. I'm not saying over look it. I would operate the engine and put 25 to 50 hours on the engine. Be aware of the operation procedures, start up, don't do long warm up's at the dock, limit long term idling, confirm that the engine is operating at normal temperatures 170F to 190F. I believe the normal operating temperature of the D4 is 185 F +/- 5F.Operate the engine at full RPM periodically. Keep a log of the 25 to 50 hours of operation. Repeat sampling, no need to change the oil at this time. Now compare the second sample to the first sample. If the trends are the same or worse it is time to look into the cause. The trends are better. Do a complete oil change at 100 hours. Repeat sampling, if the report shows trends improving then my opinion is a contaminated sample or incorrect operation was the possible cause of the poor sample report. (High Fuel %)