had the same problem, either with the objective type 'Engage all merchant shipping in...' or 'patrol x sea' - the mission objective won't complete - so I just ignored it and went home. However, I found that in one mission, upon reloading, after having patrolled the area designated for quite some time prior to saving - the mission objective was suddenly completed.
So perhaps try patrolling the area for some time, save and load the save - maybe that'll do the trick?
And yes, you can't dock at Manila in that mission (I suppose it was the second mission with the Asiatic fleet? I had to patrol Celebes Sea in that one, too), you have to make your way to Soerabaya, as Manila has been captured by the Japanese.
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