United were eliminated on penalties on Wednesday night by the League One team.
Afterwards, Jones was baffled by Amorim's system and his inflexible approach.
On Sky Sports, Jones and ex-Crystal Palace winger Jobi McAnuff criticised United's approach.
"How many times was the spare man Matthijs de Ligt in the build-up? With the greatest respect to him, you should have an attacking player joining in and getting into the box," said McAnuff.
"It just seems crazy that he (Amorim) is wedded to this formation at all costs, in any circumstances in a match that he is almost forcing people into positions no matter the state of the game. It is baffling that there is no flex at all."
Jones added: "When he (Amorim) changed and put Mason Mount in that position they still went with a back five. They were building with a back five against Grimsby who were sitting on the edge of their own box.
"(But) if he changes now it will be seen as a sign of weakness for sure."