As long as the jerking doesn't continue when she wakes up, it doesn't sound like seizures or infantile spasms, which I assume is what you're concerned about. But definitely call the pedi for peace of mind--things like that tend to freak me out!
I always have weird dreams when I'm sick and I know my kids are particularly restless when they have a fever. Poor bug probably can't get comfortable. It's good you are taking her in to be sure.
You can sometimes have pretty vivid/weird dreams when you have a fever which can cause this in some causes. I would call to make sure, but it probably isn't anything to be concerned about. Sorry she isn't feeling well