Joe Gomez has been pictured with a noticeable scratch across his face following an altercation with teammate Raheem Sterling.
Winger Sterling trained with the England squad on Tuesday, despite being excluded from the upcoming fixture against Montengro.
The Manchester City forward admitted "emotions got the better of me" following a row with fellow England star Gomez.
Despite the snub for Thursday's fixture, Sterling appeared in good spirits as he trained with his England teammates.
But Gomez flashed a noticeable red scratch below his right eye during the training session at St George's Park, Burton.
Sterling and Gomez clashed towards the end of City's 3-1 loss to Liverpool on Sunday and the pair got into another exchange after meeting up for duty on Monday.
Sterling, a former Liverpool player, wrote on his Instagram account: "First and foremost everyone knows what that game means to me! Everyone knows that I am not that way inclined and more to the point. Both Joe and I have had words and figured things out and moved on.
"We are in a sport where emotions run high and I am man enough to admit when emotions got the better of me.
Sterling added that he and Gomez "are good" and "both understand it was a 5-10 second thing it's done we move forward and not make this bigger than it is".
"Let's focus on our game on Thursday," he signed off, alongside three love heart emojis.
Southgate addressed the media on Tuesday, saying it was important he did so to keep his players out of the spotlight.
"I think I'm dealing with a very young squad and we're in a sport where emotions often run high," he said.
"Raheem in his post last night explained that, for a very brief moment, his emotions ran over and it would be correct to say that was not the same for Joe and these things happen in football."
He said emotions had to calm down and that he was helped by his senior players who helped bring the squad together.
Southgate said he had to consider what was "right for the group moving forward" and that was behind his decision to drop Sterling from Thursday's game.
"In the end, when you've made a decision like that, it's going to be public on Wednesday or Thursday anyway, I'd rather deal with it now so we can focus on the game. The decision's been made and as a group we're all moving forward."
He would not be drawn on the detail of the breakfast incident - "we don't need to add to that".
He added: "I've said what I think needs to be said publicly, but we have to keep as much as we can between ourselves."
Southgate said: "Quite a number of our senior players have been active in discussions, certainly during yesterday. I think that's an important process because I want to get a feel for where the group are - but then I'm the manager and I have certain decisions that are my responsibility and I was prepared to take."
"I love all of my players. We are like a family. The important thing is for a family to communicate and work through problems," said Southgate.
England fans - and former players - seemed to be split on England's decision to drop their star player.
Ex-England international Rio Ferdinand said while Southgate had handled most situations "brilliantly" until now, he had got this one wrong.
Writing on Facebook, Ferdinand said the current England manager should have kept this incident in-house.
"Let’s be honest now this kind of stuff isn’t uncommon in squads full of testosterone," he wrote.
"Gareth would no doubt had seen worse many times during his time as a player and manager.
"I just feel this could and should have been handled better to support the player & not hang him out to dry."
But, former international defender Lee Dixon told ITV News that he was sure Southgate had acted as news of the altercation was bound to come out.
He said that rather than "sweep things under the carpet" he had acted in the best interests of the team.
Jake Rattley tweeted: "First thing Southgate has done wrong as England manager. Hanging our best player out to dry is the most typically English thing you could do. Embarrassing on Southgates part.
Liam Murray said: "Very disappointing to lose @sterling7 for the last two games. Hope it’s been dealt with now. Although he’s the best player at the moment, the team comes first."
Former England and Manchester City star Micah Richards tweeted: "Can we get VAR for the Raheem sterling and joe Gomez situation????"
A statement from the FA said: "The FA can confirm Raheem Sterling will not be considered for Thursday's EURO 2020 qualifier against Montenegro as a result of a disturbance in a private team area at St. George's Park today. He will remain with the squad."
Manchester City and Liverpool and widely tipped as the two standout favourites to clinch the Premier League title this season.
Liverpool finished just one point behind City last season and are aiming to end a 30 year wait for a domestic league title.
City meanwhile are aiming to win the Premier League for the third season in a row under Pep Guardiola.
The clash between Sterling and Gomez is likely to dominate the build-up to England's 1,000th international fixture.
Sterling, 24, has been in exceptional form for England, scoring eight goals and providing five assists during Euro 2020 qualification.
Gomez, 22, who was introduced as an 87th-minute substitute on Sunday, won the last of his seven England senior caps in the Nations League third-place play-off against Switzerland in June.