United are through to the fourth round of the FA Cup with a 2-0 win over Wigan Athletic at the DW Stadium on Monday night.
However, there was controversy when referee Anthony Taylor awarded a penalty to the Red Devils late into the contest after Liam Shaw was adjudged to have fouled Fernandes in the box.
The Portugal international stepped up to take the spot-kick, sending Sam Lloyd Tickle the wrong way to make it 2-0 and all-but confirm the win.
But the contact was minimal while there was no VAR at the DW Stadium and Murphy was left furious with the decision.
The ex-Liverpool midfielder said live on commentary for talkSPORT: "It is horrendous.
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"It is not just Fernandes, we have seen a few of them recently.
"There is a tiny little touch and unfortunately, what we are doing by giving those penalties, is we are encouraging players to dive with any, any contact.
"Because there was not enough contact to send him over and then he puts his foot on the floor and thinks 'oh, I better go over'.
"It is an exaggerated fall, it is an awful decision and it's encouraging diving. It is encouraging players to go down."
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Fernandes' goal was his first for United since November and his third penalty of the season that he has netted.
Diogo Dalot had put the Red Devils ahead earlier in the contest but it was hardly a convincing display from the Premier League giants against a side that are 18th in League One.
"He's been good tonight, Bruno," Murphy added. "Some might think I am digging him out because it is Bruno Fernandes but if it is any player that does that.
"It is the reason they do it, and the reason they keep doing it because the penalties keep being given.
"Contact does not mean penalty. Contact does not mean you have to go over.
"Yes, the lad should not have dived in but as soon as he touched him, he could have stayed on his feet but he dived, fell over."
United now face a potential trip to non league as they take on either Newport County or National League side Eastleigh in the fourth round.