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That's not adequately answered. The most reasonable answer is that he's not held back an entire year, but rather did some sort of remedial and took the exam again, like, a couple weeks or a month later, and there was a gap between the final exam and team assignments. But that's speculation.
You take the exam as many times as you need to, you don’t have to repeat a year to retake the exam or anything like that
I checked the japanese, and Iruka doesn't specify if naruto failed the graduation exams, but just refers to them as exams. And now it's going to be the graduation exam and previous grades don't matter.