The order of unrestricted warfare was given when the war started so we sank cargo ships, tankers, transports etc. in addition to warships. I'm trying to find the reference but I read somewhere that after one of the sinkings of a POW ship that we decided to let go any transport that appeared to be headed back to Japan thinking that it could be carrying prisoners. Everything else remained open game.

Not exactly POW related but does relate to the targeting of ships marked as non-combatants.

Takasago Maru (Wiki)

I didn't realize that we let Japan send a hospital ship to Wake Island during the war. We inspected it both in and out but didn't stop it. This was when we had bypassed Wake Island. We did damage the hospital ship a couple of times previously but in several other attacks hit only warships around it. It and another hospital ship are the two largest Japanese ships to survive the war.

We sank the Awa Maru on April 1, 1945. We had granted safe passage of the ship to deliver Red Cross relief supplies. She was to have white crosses on either side of the funnel. Two white crosses on each side of the ship were to be illuminated at night. All navigation lights to be on. The schedule and route was sent out several times. The sub still mistook her for a destroyer.

YZ250 said:

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The order of unrestricted warfare was given when the war started so we sank cargo ships, tankers, transports etc. in addition to warships. I'm trying to find the reference but I read somewhere that after one of the sinkings of a POW ship that we decided to let go any transport that appeared to be headed back to Japan thinking that it could be carrying prisoners. Everything else remained open game.

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There is nothing in Clay Blair's Silent Victory about this. Don't think it happened b/c they US Subs were sinking just about everything in sight in 1944/1945.