What was your physical location when you attacked? If they were near the end of their trip the whole convoy may have vanished and you weren't in a position to see it. They can't reorganize and sail into port, so the game has them disappear at their last waypoint.
Also, what was the weather? There is a chance that the crippled ship sank due to heavy seas and you didn't get the credit. Always look at the map. A grey sinking mark will tell you if that happened.
As to the neutral ship, the game isn't that sophisticated. It doesn't matter what the cargo is. If it's flagged as a neutral then it's neutral, and BdU doesn't really care what you think.
