The conversation occurs after A did B a favor:
A: I'm glad I was able to help you out! B: You're glad!
What does B imply?
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It depends on how much stress was put on each word.
Would imply that person B thinks he/she is the one who should be thankful, not person A. As in "Why are YOU thanking me! It surprises me to see YOU thanking me! I'm the one who should be thanking!"
Implies that person B didn't think that person A would thank them, because he/she thinks what they did was not worthy of being thanked for, or they think what they did was rather destructive than helpful and thus, it surprises them to see person A thankful. "You're GLAD? I thought you would be mad at me!"/"you're GLAD? But I messed up!"