Like people were alive under the ocean trapped... Alive? They die of lack of air or something while down under the water in a submarine that is whole and experiencing technical issues or something.
I think you may need to clarify this question.
The US lost 52 submarines just during WW2. Many of these were sunk by enemy fire, but many were also lost to "storm or perils of the sea."
It seems your question is specifically whether a submarine has lost its mobility and hit bottom while its crew was still largely unscathed, resulting in a slow death of the crew.
You could read about the HMS Thetis, which suffered a technical malfunction during an excursion, claiming the lives of its entire crew. Noteworthy is that it was then recovered and recommissioned later.
The K-141 Kursk was a Russian submarine. It suffered an explosion during a exercise and sunk to the bottom. Reports suggest as many as two dozen of its crew died of suffocation and not as a result of result of the explosion itself.
I'm sure there's other answers, too. Maybe a military historian could come up with something comprehensive. I'm quite confident the answer to your question is "Yes," though.
Slow suffocation may have happened to the H.L. Hunley, an early submarine deployed by the Confederates in the US Civil War.
Scientists found the eight-man crew of the hand-cranked Confederate submarine had not set the pump to remove water from the crew compartment, which might indicate it was not being flooded.
That could mean crew members suffocated as they used up air, perhaps while waiting for the tide to turn and the current to help take them back to land.
The Hunley was sunk after an attack on the Housatonic. It was previously thought that it was too close to the exploding torpedo and took damage.