What matters is the reason why he was flagged. Unless the Soldier is new to the Army and doesn't know any better, then his NCO should have informed him upon the day the action took place. There are many reasons why a Soldier would be flagged...ie. failure to maintain weight standards IAW AR 600-9, APFT Failure, recent UCMJ actions. Besides, ifa Soldier is flagged, he should have received a written counseling by either the CDR, 1SG, or his first line supervisor stating the reason why he is being flagged. That is the right thing to do.
If he's trying to take college courses, a company commander will not allow him to take college courses because of the flagging action. Most commanders believe that if the Soldier has the time to take college, they also have the time to take the initiative to improve their deficiencies (losing weight...working out...etc).
If he doesn't know what he's flagged for, he can look on his ERB. On the left side, there is a portion that contains flagging actions. There should be a 2-letter code. For example, "KA" is for weight failure. His training NCO should have a list of all the flagging actions. Once a flag is removed, it will then state "KE" on his ERB and will remain on his ERB for 3 years...I think...not quite sure of that last part.
Most of his questions can be answered by his company orderly room...but as to the original question...most Soldiers KNOW when they're getting flagged. If he looks up the code and finds out that it was put on his ERB erroneously, his commander has to sign the DA Form 268 in order to remove the flag. Hope this helps. :)