Is this dialogue OK?
Person A. There is a $ 100 outstanding balance from last time.

Person B. Are you sure there isn't some kind of mistake?

Question

Is this dialogue OK?
Person A.   There is a $ 100 outstanding balance from last time.

Person B.   Are you sure there isn't some kind of mistake?

Answer

Those are both acceptable.
The first sentence might be better substituting "after your last transaction" for "from last time". But an English speaker or reader would understand both of  your original sentences.

Answer

good, but only one correction: Tenses are not complimenting each other here, Are you sure there isn't some kind of mistake?

Other ways to say this:
"are you sure there WASN'T some kind of mistake?" 
"Are you sure there HASN'T been some kind of mistake?"
"Are you sure THIS isn't some kind of mistake?"

hope this helps!!