Was it night and/or rain?
I've had it happen occasionally. You are to far away to "see" the ship, thus no credit is given or marks made on the map. I just had this happen at night, a few days ago in SH4. As I was heading away, the ship, which took some 4 hours(game time) to sink, finally went under. Even though I watched it sink, through the binoculars, I was too far away, thus no credit was given in the captain's log and no sinking ship mark was made on the map.
Sorry, but it is just how the game functions. It can be a real bear at night in bad weather.
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