Before the clash with Elche on Tuesday night, Mbappe, Konate and Vini Jr semi-obscured a message reading "we are all Ceutans", referring to the people living in Spain's North African territory.
This act came after more than 70,000 irregular crossings into Ceuta from neighbouring Morocco in July where according to The Telegraph, crime had now increased eightfold.
Most of them returned in the hours following their arrival, but several thousand remained in Ceuta and reportedly remain homeless in the territory.
Real previously staged a tifo display in their singing section during last Tuesday's Champions League match against Inter Milan, where supporters held up placards depicting the Ceuta flag.
Speaking on the slight protest from the trio, Mbappe revealed that his stance was that he supports the people of Ceuta, but he accepts that many had died as a result of the crossing.
He told AS: “I want to explain this clearly so people understand. It was the club's decision to include the jersey, to have us wear it. We players had to wear it. The first thing I want to say is that I stand in full solidarity with Ceuta and with all the victims.
“Because before I’m a player, I’m a human being. But I also wanted to make a gesture and spare a thought for all the immigrants who have lost their lives and who are also living in harsh conditions.
“It wasn’t an easy position to take, it was difficult because in the end, people might think I’m against the people of Ceuta, but no, absolutely not.
“'I have nothing against them, and I support them 100% in my thoughts. But I also wanted to spare a thought for all the people who are suffering, because at the end of the day, I’m human, and I don’t want to prioritize one form of suffering over another.
“There are people who are suffering, and it breaks my heart to see that happening in the world. I’m a young man who wants the best for the world we live in.
“I aim to send a message of positivity and peace, and I hope this situation is resolved quickly.”
Real Madrid went on to win Tuesday’s match and the side next face rivals Atletico Madrid this Sunday where Mbppe should start once more.