I was also stressing about one of my fish that recently came through the mail. She was gasping, very lethargic, and only came up once in awhile to breathe. I lowered her water levels, added a bunch of oak leaves, and put plastic wrap around her tank. She's been perking up and flared at a few neighbors she could see. :)
More CO2 accumulates in the bag the longer the fish are in there. The when dissolved in water, CO2 separates into Carbonic Acid and Hydrogen. The Carbonic Acid lowers the water pH, which then neutralizes the Ammonia build up. When the bag is opened, O2 rushes in which then makes the Ammonia toxic again. You may be seeing effects of Ammonia poisoning as well as stress.
I'm sure they will be fine :)