The Daily Mail says Amorim was angered by Garnacho's actions when substituted during the Europa League clash with Viktoria Plzen.
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Since then, Garnacho was dropped for the derby win at Manchester City before being left on the bench for the past four games.
Club sources insist Amorim isn't unhappy with Garnacho, but has major demands that all players must adhere to.
The 20 year-old's situation has also led to claims he doesn't fit into Amorim's 3-4-3 system.