There's a little bit of engine oil left in the system which has soot and carbon in it. It's enough to turn the oil dark. I think there are some more notes in the oil change article for common rail engines.
Also, the service manual says the oil filter should be removed before draining the oil pan because it releases a one way button in the filter housing, letting the oil in the filter circuit drain into the oil pan. It's probably only a cup but it's more than enough to turn the oil dark.
Black oil is normal on a diesel because higher piston blowby and soot turns it dark. It's still doing a good job even though it looks dirty.
Also, the service manual says the oil filter should be removed before draining the oil pan because it releases a one way button in the filter housing, letting the oil in the filter circuit drain into the oil pan. It's probably only a cup but it's more than enough to turn the oil dark.
Black oil is normal on a diesel because higher piston blowby and soot turns it dark. It's still doing a good job even though it looks dirty.