Neville was left stunned with the lack of communication between the players in the dying stages.
He said on The Gary Neville Podcast: "Smalling has got to flag up as an experienced defender that he's struggling, get someone else into the centre.
"It didn't happen for two or three minutes.
"Then Phil Jones recognised it had happened and tried to reorganise - as I saw it, Ander Herrera refused to go to right-back and told Henrikh Mkhitaryan to go back there. All over a sudden Smalling sits down on the floor and then goes off the pitch and then comes back on at centre-back. He ends up picking up Harry Maguire.
"You can't believe the disorganisation and lack of leadership shown by Manchester United at the end of that game in a game they should have won. Jose will be furious when he watches that back."