The second form, “Wasn’t it ...?” is a rhetorical question. You expect the answer to be “yes.”
The first form, in written English, is a normal question that could be answered either way. In spoken English, you’d use different of tones of voice to hint that you think the person ought to disagree, that they ought to agree, or that you’re sincerely uncertain. You might indicate those with emphasis: “Was this supposed to be cupbard?” should be read aloud with the word was in a higher pitch, to mention only one way. You could also indicate this through word choice: “Was this really supposed to be ...?”
In this context, pointing out a student’s spelling mistake, making it into a rhetorical question was probably intended as a more polite way of saying, “You misspelled ‘cupboard.’” This further implies that the writer did know, and just made an accidental, minor typo. But the teacher doesn’t want to leave any ambiguity about whether it’s an error. Therefore, I think “wasn’t” is clearer. However, in many other situations, a rhetorical question could come across as rude, or even sarcastic. So use them with care. The “was” variant is gentler, but doesn’t communicate as clearly that there is a problem that needs to be fixed.