"Do you have some pepper?"
Yes, it does actually mean "do you have pepper?", but just changing into genitive is incorrect. You would need to add „trochę”, just as martiankoolaid suggested. The literal translation of „masz trochę pieprzu?” is "do you have some of the pepper?".
We just don't really use „trochę” that much. Well, perhaps neither do English speakers, but the course creators cannot alter the English sentences on the course, only its Polish translations.