Boufal is alleged to have angered his manager when refusing to warm up during the Saints' 3-2 loss to Chelsea in the Premier League on April 14.
Having started Hughes's first two matches in charge, the 24-year-old has now been left out of the squad for the last two matches, including last weekend's FA Cup semi-final against Chelsea.
Asked to comment on the incident at his pre-match presser ahead of the Bournemouth match on Saturday, the Welshman told reporters: "He made a mistake which he has acknowledged to me since. At the moment he is training with the 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 teammates and that is the process we are working towards. He won't be involved this weekend."
Boufal has played a direct part in just four Premier League goals in 26 appearances this season.