Never had either one of mine get scabs from a shot. Only time is if they get into a rough play time or something of the sort. I keep an ointment called Vetericyn as part of my "first aid kit" for my furbutts. It's really good for minor cuts, burns, sores, etc...
Amazon.com : Vetericyn Wound & Skin Care Hydrogel...
Since your furbutt's on antibiotics, as long as you don't notice signs of illness, I think she should be fine. Also, you said she'll be getting "a set" of shots? How many will she get? Being so small, it might be better to spread the shots a bit.
Magnus (16 lbs) does fine with him but Zoey (5.5 lbs) gets so out of it whenever she gets a shot. I usually spread them about a week or so apart so she won't be overwhelmed.
Good luck and hope your girl heals quick!