There is a small amount of fuel in almost every oil sample. If my memory doesn't fail me, it is acceptable to have 3 to 5% fuel dilution. Diesel is actually a pretty good lubricant, otherwise fuel pumps and injectors would fail rapidly. Most of it comes from unburned fuel in the combustion chambers.
The 1983 to 1985 6.9s had a problem with the injection pump shaft seal that would allow fuel to get into the oil. Stanadyne installed a double shaft seal and a weephole on the front bottom of the pump that solved the problem. Now if the seal fails, fuel leaks out onto the engine.
The fuel transfer pump also is designed to prevent fuel from a bad diaphragm from entering the crankcase by having the lever opening above a weephole