His remarks follow United's chastening 3-0 defeat to Manchester City at the Etihad Stadium on Sunday, a result that has further intensified scrutiny on Amorim after a stuttering start to the season.
United have managed just one victory from their opening four matches, with their shortcomings laid bare in a lacklustre performance against their local rivals.
Despite making several additions in the recent transfer window, United failed to strengthen in central midfield - an area that has remained a persistent weakness under successive managers.
Instead, the club opted to bring in two number 10s, Bryan Mbeumo and Matheus Cunha, a decision that has forced Fernandes into a deeper midfield role.
Last season, the Portuguese international was one of the few bright spots during a troubled campaign, often carrying United with his creativity and leadership. But this term, operating at the base of midfield alongside Manuel Ugarte or Casemiro, he has looked increasingly ineffective.
Against City, Fernandes' struggles were highlighted when he allowed Phil Foden to drive into the box unchallenged to head home for the Sky Blues.
Scholes believes Amorim's style of play is exposing the weaknesses in Fernandes's game, instead of highlighting his strengths.
"The big question will be about Bruno and his position I think. Having him as one of the central midfielders... look, he's United's best player there's no doubt about it, on the ball he's brilliant, but going to Man City against a Pep Guardiola team - it took me years to adjust to that position," said Scholes, according to the Manchester Evening News.
"I needed someone next to me that knew the position brilliantly, Nicky (Butt), Roy (Keane) or Michael Carrick.
"You get away with it in 80 percent of the games but you play the best teams, you don't know where you are.
"You don't know that position so you don't do it and that's what Fernandes is like, he's lost a little bit.
"He's trying to do too much and I think it's taking away his quality.
"You have to go back to recruitment in the summer for that, they bought two number 10s, did they need two number 10s?"
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