Hughes has resolved the situation with Boufal, but has confirmed that the 24-year-old will not feature in Saturday's vital home game against Bournemouth.
The Saints boss said: ''He [Boufal] made a mistake which has acknowledged to me since. At the moment he is training with U23s but he has missed a few days because he was ill.''
"Given where we are at the moment, he is probably best served just training with a different group just to make people aware it shouldn't have happened.''
"He understands that now and he probably needs to build a little bit of trust with his own team-mates and that is the process we are working towards. He won't be involved this weekend [against Bournemouth]."
The Bournemouth clash is crucial for Southampton's battle to avoid relegation, being four points from safety with only four games remaining.
Hughes admitted: ''It is clear to us, this is a black and white situation and we need to win the game. Clearly we need three points. It has been a long time coming. We are well into the business end of this season and it is time to get business done.''