I'm sure you are.

[Ashraful Haque]

"I'm sure you have/are."
Everytime I hear this in movies/shows, I get a bit confused about whey they said it. I feel like it can be said both in a polite and in a sarcastic way.

Sarcastic-
Mom: Who broke the plate?
Child: The cat did it.
Mom: I'm sure the cat did it (realising that the child is lying)

Serious:
Parent: My son is very serious about his studies.
Principle: I'm sure he is.

NB: I made up those sentences by myself. Please correct me if they're wrong.

 

[Barque]

Child: The cat did it.
Mom: I'm sure the cat did it (realising that the child is lying)

More likely--I'm sure it did. You don't have to repeat "cat" or "it".

Serious:
Parent: My son is very serious about his studies.
Principle: I'm sure he is.

Yes, this is fine. It could either be serious or sarcastic. And it's "principal", not "principle", in this context.

I get a bit confused about whey they said it.

The context should tell you what's meant.