At the end of the story , What internal conflict does Caline experience ?

Yes, Caline liked the woman for whom she was working.

"The flagman's sister was a kind and gentle task-mistress."

Caline's internal conflict comes from the fact that she moved to the city for the wrong reason and hadn't even realized it.

"When the woman asked her again after another week if she were still pleased, she was not so sure. And again when she questioned Caline the girl turned away, and went to sit behind the big, yellow cistern, to cry unobserved. For she knew now that it was not the great city and its crowds of people she had so eagerly sought; but the pleasant-faced boy, who had made her picture that day under the mulberry tree."