There appears to be a large amount of smoke drifting by visible in front of Union soldiers in Battery Stevens. Perhaps from other guns of Battery Stevens?
Only titled "Bombardment of Ft. Sumter" at LOC. I see a fragment of a Haas and Peale signature at the bottom right of the photo on the uncropped LOC version. They of course famously photographed from Morris Island smoke coming from the USS New Ironsides while it was firing at Fort Sumter in September 1863.
Here is a print of the from another negative of the same section of Battery Stevens taken at another time showing no smoke in the background. It also shows that the negative was originally by Haas and Peale: http://digital.hagley.org/islandora/object/islandora:2372922
Could the smoke and dark areas in the sky are actually a product of the degradation of the emulsion over time?
Here is Miller caption for the second print: