Baleba, who remains on Manchester United's shopping list, was visibly upset after being benched by Hurzeler.
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After the 1-0 defeat, Hurzeler stated: "I'm not happy with the yellow card he gets so absolutely the wrong decision for me to give him… the first foul wasn't even a bad foul, not a tactical foul, a yellow card.
"Then of course we had to take care of him so that was the only reason. But it was a big impact from the referee to give that yellow card, therefore we had to make the substitution."
Brighton blocked the Cameroon midfielder from joining United over the summer and warned them off ahead of last month's winter market.