Don't freak out about a little bit of caffeine one time.
It's not like you accidentally gave her oxycontin or something dangerous. She'll be fine.
As for her temp -- why is she constantly taking her temp? Does she not feel well? If so, then THAT's a concern. But everyone's baseline temp is different. 98.6 is just an average normal. For me, my temp is normally about 98.0 when I'm not pregnant. All the hormones make it stay higher during pregnancy. I don't know what mine is now, because I don't really care enough to get up and go test it -- lol!
As the other poster said, there are lots of new experiences with pregnancy, including odd aches and pains, extra gas and bloating, sleeplessness and sleepiness, and more! Try to remember that throughout this special time. If something REALLY has you concerned, then definitely called the doctor -- they expect it and aren't bothered by phone calls at all.