My kitten gets the same way. The vet said it makes her sore and and her whole body hurts. My vet said it is a bad reaction and that is just how some animals react.
You should consider calling the vet or taking her back in. Sometimes issues come up with vaccinations. It's not common, but the injection area can react badly, leading to localized scarring and infection that can be very painful and cause life threatening problems down the line.