Yip, 3" nails!
No idea what they are doing there. I can only assume they were welded on the box section before and he just didn't bother to cut them off but 3 of them look as if they have been used a filler material.
Yes, why do people spend more time bodging a job than doing it right in the first time and saving time (and probably money as filler/bondo isn't that cheap).