The Whites trailed 2-0 at the interval and boss Marcelo Bielsa opted to make a double change during the break having earlier replaced the injured Stuart Dallas with Leo Hjelde in the ninth minute.
Tyler Roberts and Adam Forshaw were brought on as United’s final two substitutes but star man and top scorer Raphinha was one of the players withdrawn along with Mateusz Klich.
Bielsa confirmed afterwards that the substitution of Raphinha was tactical, the head coach wanting to send Roberts upfront and move Dan James from the no 9 role to replace Raphinha on the right wing.
Murphy, though, could not understand the decision and felt Raphinha was causing Jonjoe Kenny issues down that side of the pitch.
“It was a mistake,” said pundit Murphy of the Raphinha change on Match Of The Day.
“He can explain but all right but he was showing and causing Kelly a good few problems.
“Okay, he hadn’t scored or set up a goal but you are 2-0 down in a game and you need your best players.
“Maybe he was setting an example for something or he saw or an incident but I didn’t see enough in that first half performance to warrant him being brought off.
“It was a really strange decision.”
Leeds went on to suffer a 3-0 defeat and failed to land a single shot on target.

1. PSG plot Diop swoop
Ligue 1 giants Paris-Saint Germain are reportedly set to offer West Ham United as much as £50m in exchange for defender Issa Diop. (Various) (Photo by Laurence Griffiths/Getty Images) | Getty Images

2. Man United keen on Nkunku
Manchester United are exploring the possibility of signing RB Leipzig midfielder Christopher Nkunku this summer. (ESPN) (Photo by RONNY HARTMANN/AFP via Getty Images) | AFP via Getty Images

3. Palace face Zaha battle
Crystal Palace are facing a battle to convince Wilfried Zaha to sign a new contract. The player’s deal expires in summer 2023, but the 29-year-old is not planning to sign an extension. (Daily Mail) (Photo by Dan Istitene/Getty Images) | Getty Images

4. Brighton still keen on Rodon
Brighton could look to rekindle their interest in Tottenham defender Joe Rodon at the end of the season. Leeds United have also been linked. (SussexWorld) (Photo by Mike Hewitt/Getty Images) | Getty Images

5. Sevilla expect Carlos interest
Sevilla fully expected Newcastle United to ‘return to the fray’ with another offer for Diego Carlos this summer. (Marca) (Photo by Fran Santiago/Getty Images) | Getty Images

6. Reds keen on Bissouma
Liverpool want to sign Brighton midfielder Yves Bissouma this summer. (Mirror Football) (Photo by Mike Hewitt/Getty Images) | Getty Images