It is always hard when your bff is dating someone and you are not. She probably feels like a third wheel at times. If you and your boyfriend have a good relationship, she may sometimes wish she had that with someone too. Just reassure her that you are still great friends and prove to her that no boyfriend will come between you two. Just try to put yourself in her shoes and understand where she is coming from. Even if you don't totally understand, her feelings are her's and are still justified. Don't let this ruin your friendship. Good luck :)
I think she might be feeling this way because she sees that you area having fun with your boyfriend which might not be the case for her. Again, you boyfriend might be portraying what she loves most in a guy yet she knows that she can't have him. Try and avoid spending time with her when you are with him.
I would say that yes she might feel like a third wheel. Spend less time with her around your boyfriend but still spend time with her. If she still acts the same talk to her about how you feel. She may have been used to not sharing you.