A rift between captain Harry Maguire and Cristiano Ronaldo was reported ahead of Monday's (AEDT) clash with Leeds United.
But Marcus Rashford and Maguire each responded on social media, while interim manager Ralf Rangnick described the claims as "absolute nonsense," before saying the 4-2 victory was the "perfect response" from his players.
Fernandes has also now denied the story, saying the togetherness and camaraderie of the group was evident in their goal celebrations at Elland Road.
"It is honestly people trying to complain and making stories about this club,"the Portugal midfielder said. "I don't know what people mean. I saw the goal of H [Maguire] and saw Paul [Pogba] running behind, sliding on his knees, happy for him. I was slapping his head and saying finally he had scored with that big head.
"We know when someone talks about this club or players at this club, it goes around the world with their voice. That is something that they want.
"For us, it is nothing. If we stick to the plan and stick together, that is the main thing: losing together and winning together."