Some injections do sting a bit and she was obviously stressed. And concerning vaccines in the future - my vet was giving one of my girls an injection of some kind recently and was giving it in the rear area. I had been taught to do any sub-q injection in the neck and asked him about it and if it was because of SM. He said that studies have shown that the medication is absorbed much more readily if given in the rear than in the skin around the neck. I certainly wouldn't feel shy about talking to the vet about it.
Glad all is doing better with your baby. We went through a bout of hemorrhagic gastoenteritis a couple of years ago and thought we were going to lose Tibby.
RIP Wallis, John Robert, Tibby & Pip
Mom to JoJo, Roxie & Linguini (Cavaliers)
and my birds Moji (Senegal) and Walter (Blue Front Amazon)