It’s true that some girls will become interested in you if you compliment them. It is common with lots of girls and guys to react differently from others. She might tell you to stop hitting on her in a friendly joking manner.
But if she is embarrassed about it, rather stop right there, apologize and tell her that you are not into her. But be completely honest and gentle.
Be firm that you were just being friendly and building a friendship. Some women will see a compliment as an intimacy cue and some will see it just as you being friendly.
Let her know she has the wrong idea without embarrassing or shaming her.
One friendly compliment you could use here to end it is "You're a nice, smart girl, but I like you just as a friend, not a girlfriend. I hope you're OK with that."