Barca have axed Xavi just a month after the Catalan had reversed a decision to resign at the end of the season.
Sanchez Flores said: "I shouldn't say this... But Barcelona treat their legends so badly.
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"With (Ronald) Koeman, with (Lionel) Messi, with Xavi now. I wish clubs treated their legends well, incredibly well. It would have been fantastic. "
Hansi Flick is set to be confirmed new Barca coach.
The German coach will sign a contract to the summer of 2026.