Fernandes was United's star player in 2020-2021, as they finished second in the Premier League.
However, the arrival of Ronaldo resulted in a downturn in form for his Portuguese teammate.
Fernandes only managed 10 Premier League goals, after netting 18 the season before.
"I think at the start of the season, he [Ronaldo] created a problem straight away with [Edinson] Cavani," Neville said on Sky Sports' The Overlap.
"[Cavani was] being pleaded to stay and lead the attack for the year, but when they signed Ronaldo, Cavani was shot then and finished. It upset the dynamic in the dressing room for Bruno.
"I think Bruno looks up to him like a godfather in Portugal so it made him feel a bit inferior to what he was before. It made Maguire a little bit inferior as captain just naturally – nothing from Ronaldo's doing this.
"Just his presence itself on the pitch means everyone's looking to Cristiano with Harry trying to establish himself as United captain.
"I don't know where the cliques are, I'm not close enough to it but you mention words like 'rotten' 'broken'.
"Harry Maguire has gone from someone who I think was growing on the pitch last year in Covid to someone who looks like he's shot to pieces when he pulls on a red shirt.
"Bruno looks like half the player.
"The rest of them, the young players, it looks like you've lost complete faith in them, let's get rid of them.
"That's when something has gone fundamentally wrong in the changing room, in the leadership, and I don't think you can absolve anyone of blame. Everyone has to take blame for that."
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