if he is in f1 and didnt work in school and have filled out 1040A and have gotten $1000 then he could be in trouble. Not in the sense that he will get deported or anything like that, but IRS can actually get in to his account and get that $ he have + the interest that have incurred during that time. These cases are really rare, if many students keep filling 1040A, which is primely for those who are qualified to work in US, Then IRS will start audit soon cuz they will have a budget deficit. had be been filled different form other then 1040, then i don't think there should be any problem.
not a pro on this matter, just an opinion which can be WRONG.