Actually there weren't really any new rules on the treatment of prisoners during the Civil War I think. In any case neither side treated their prisoners particularly well with Andersonville being but the most extreme examples.
In the US Civil War many inventions that had been made before and even been used in war before on smaller scale were for the first time used on a large scale. The use of rifled guns which through the invention of the miniÈ ball were for the first time as quick to load as smoothbore muskets and not as prone for failure may have been the most important one, but the invention itself had been made in the 1840s already.
One invention that was for the first time used during the Civil War but on so small a scale that it did not have any notable effect was the machine gun. During the Peninsula Campaign of 1862 several Agers Guns (sometimes referred to as Agers coffee mills) were used by the Federals, but it was purely experimental and same as with the testing of some of the more famous Gatling guns in the later phase of the war the commanders showed very little interest in these innovations so the effect was very limited.
Another thing that had been used before but was used here on large scale for the first time (same as the railroad) was the telegraph which allowed news to travel much faster. Possibly even more important was the use of photography and the publication of photos. There had been photos of the Mexican War and the Crimean War already, but in the Civil War photographers such as Matthew Brady and Alexander Gardener really brought home the grim face of war for the first time. Percussion caps (rather than flintlocks) are another invention made some 30 years prior to the war but were use there on large scale for the first time making firing a gun in the rain more likely than with the flintlock guns (though it didn't work in every weather conditions either). The same also goes for repeating rifles where the most important inventions had been made before the war but which were used on large scale (but not as "standard equipment to the end of the war") for the first time.
The size of cannons, especially of siege mortars also reached a level unheard of before the US Civil War. Railway guns were indeed used for the first time there.
The Civil War also saw the first case of a ship (the USS Housatonic) being sunk by a submarine (the CSS Hunley) which was also lost in the process. There had been experiments with submarines before and even the attempt to sink a British ship in the war of independence with the submarine Turtle, but here a submarine succeeded for the first time.
The Civil War also saw the use of anti ship mines (then referred to as torpedoes) for the first time and there was also the little effective use of a kind of landmines (I don't really know if something like that hadn't been used before).
Barbed wire was for the first time used for military purposes in the battle of Knoxville.
Balloons also saw limited usage in the Civil War (they had been used in the French Revolutionary war however) and one may consider the deliberate use of cannon trying to shoot down balloons as the invention of "anti aircraft fire".
Most of the innovations of the Civil War had been invented before and were just used on large scale for the first time there (in my eyes an example for the mistake in the believe that war provided as extreme an increase of development as is so often claimed).
