The Battle of the Atlantic was characterized by open ocean operations in deep water. Coastal actions occured, but tended to be limited, and running aground in hostile waters was rare.

In the Pacific, submarine operations tended to be in shallow waters. The Pacific is dotted with shoals, coral reefs, and various shallows that were poorly mapped at the time. More than a few submariners grounded during WWII. Several subs got stuck so hard that they had to be abandoned. This was not a matter of crew incompetence, but rather of aggressive actions in poorly chartered shallow waters.

To make a plausible plot for a U-boat, the sub would need to be operating in poorly marked or unknown shallow waters, probably on the surface, and therefore at night. Maybe a recon mission, or maybe landing some spy agents, would be a good example, or a mining mission. Say the sub snuck in at night underwater, did its business, and then snuck away. After a mile or two, it surfaced to make a faster surface run, and BAM!, it runs into an uncharted shoal good and hard.

As for ideas that the allies could plant to lure a sub into shallow waters, here is one. The German U-boat POWs had a code in their letters hom by which they sent secret messages. This code was known to the allies and broken and easily read. There was one incident where U-boat POWs plotted an escape, and coordinating via these letters, Doenitz sent a U-boat into the shallow St Lawrence River area to rondevous (sp?) and pick them up. It didn't work out, as the plot was discovered by the allies and the escape thwarted.

But you get the idea. The allies, using the letter code, plant a story of a POW escape to the U-boat command - could a U-boat meet us at this point (a plausibly selected spot in some shallows - on a night where night is high tide). Doenitz was dedicated enough to his men that he'd risk a boat to try to rescue some POW's. At the appointed time the U-boat shows up, but it's a trap. Coast Guard Cutters and Destroyer Escorts show up and block there escape. The water is too shallow to escape underwater - the boat makes a high speed run for its life on the surface, dodging among the shoals close to shore to try and escape around the encircling escorts till WHAM!, they run up on some sandbar. As dawn comes the tide is ebbing, they're surrounded, and there is no hope.

You get the idea.