The Manchester United captain required treatment in the closing moments at the Stadium of Light after Sunderland substitute Nilson Angulo appeared to catch him in the face with a raised arm.
Despite protests from Fernandes and several United players, Attwell allowed play to continue.
VAR official Peter Bankes also chose not to intervene.
The decision sparked anger inside the away dressing room after full-time, with Fernandes understood to have voiced his frustration to team-mates and coaching staff after another officiating call went against United.
Manager Michael Carrick admitted his captain was unhappy, although he stopped short of directly criticising the officials.
“Bruno said there was contact and he wasn’t too happy about it when he came in.”
“The staff on the bench weren’t too happy with it as well.”
Carrick then hinted at wider confusion over refereeing standards.
“I’m getting a little bit confused with what’s going on really.”
The incident is the latest flashpoint involving Attwell and United after club officials previously lodged concerns over a penalty decision in the 2-2 draw with Bournemouth earlier this year.
For Fernandes, patience appears to be wearing thin.
And for United, the feeling is growing that too many key moments are slipping away without explanation.