Rafael was facing his former side for the first time since he was sold to Lyon in 2015 by Louis van Gaal.
The decision irked many supporters, who held the Brazilian in high regard for his energetic and impassioned displays for the club.
Ferdinand played alongside Rafael for four years and United struggled to replace the Brazilian after his departure, with Matteo Darmian failing to impress following his arrival from Torino before auxiliary right-back Antonio Valencia took over.
Rafael put in a great performance as Basaksehir recorded their first every victory in the Champions League against an awful United on Wednesday night and Ferdinand tweeted after the game to express his regret that the Brazilian was sold.
‘We never should have sold Rafael #facts,’ tweeted Ferdinand.
The former England captain then followed up the tweet with a dressing down for United’s defending from Demba Ba’s opener in Turkey.
The former Chelsea forward was somehow left completely free from a United corner and he was allowed to run in on goal to score the opener.
‘The goals against us….please tell me someone is going nuts in that changing room and people are being made accountable,’ said Ferdinand.
‘The shape of the team when we lose the ball for the 1st goal’.
Mauricio Pochettino is keen to return to management and the club may be tempted to hire the Argentine should United lose on the weekend, with the club currently 15th in the table.