if she has been properly taking the pills like you describe, then she almost certainly not pregnant, though if wouldn't be a bad idea to take a home pregnancy
test just to make sure. assuming that it is negative, she probably missed her period because of the pills, as sometimes when someone is on the pills for a while they may not have any bleeding with their period.
the symptoms will usually resolve in a few days, but if they persist, she might want to talk to her doctor about switching to a lower dose of pills which could help minimize the possibility that her symptoms are a side effect of the pills.
please let me know if you have any more questions.