The Manchester United legend's side, who are eyeing promotion to League One, lost 3-2 away at Crewe Alexandra on Wednesday night.
Advertisement
Chris Long scored a penalty in the 11th minute of stoppage time to seal the win at the expense of Bradford.
In a clip from the match, the forward can be seen walking towards Hughes on the touchline.
Advertisement
He then attempts to shake hands with the former Wales international but was denied, before patting him on the back.
Hughes then came face-to-face with Long and appeared to exchange words, with coaching staff having to come in and separate them.
However, after some pushing and shoving, Hughes was still shouting towards the player as they walked onto the pitch, before they eventually went different ways.
Bradford went 2-0 down against Crewe before netting twice in the opening nine minutes of the second half to level the score.
Advertisement
Advertisement
A point would have seen them rise to fifth in the League Two table, but Long's late goal ensured they left with nothing.
Victory for Bradford would also have kept their automatic promotion hopes alive, with the play-offs now looking more likely.
Advertisement
They face champions Leyton Orient at home on the final day of the season as they eye a return to the third tier.
Hughes has been Bradford manager since February 2022, with the club being the first he has managed outside of the Premier League.
He is set to guide them to a dramatic improvement upon their 14th place finish last season.
Advertisement
Bradford were relegated from League One in 2019, but could very well be on their way back despite the late goal on Wednesday night.