Jones has worked inside United's academy and says the tactics employed by age group teams do not mirror Amorim's system.
He told Freebets: "One of the questions I asked was why the youth and academy teams didn't play the same system that Amorim was bringing in at senior level.
"These kids need to learn how to play in different positions and in different systems to have a career in the game.
"Hopefully they do go on to have a career at Old Trafford, but if they are going to have any success in the game then they need to be adaptable.
"I think it's good for youngsters to play in different positions and systems. But there definitely has to be an alignment right through the academy so that it prepares players for the first team.
"If a player gets a call into the senior squad - which has happened for years and years at United - they have to be ready to play the system the manager employs. They have to have an understanding of it."