The striker was a second-half substitute in the fifth-round clash but was unable to complete the game after picking up a knock, while Cameron Borthwick-Jackson also picked up a problem.
Speaking on BT Sport after the game, Van Gaal said: “It is unbelievable because Borthwick-Jackson, I changed him at half-time because he was injured.
“I changed [Juan] Mata to give him a rest and also [Anthony] Martial – and then the substitutes are more less again injured.”
Van Gaal also refused to confirm whether David De Gea would be fit for Thursday night’s Europa League clash with FC Midtjylland after the goalkeeper suffered an injury in the warm-up to last week’s European game.
He added: “I don’t know. It is not so heavy but we have to wait and see whether he can start again.”
United took the lead thanks to Chris Smalling’s scuffed shot in the 37th minute.
Juan Mata made it 2-0 with an 18-yard free-kick on the stroke of half-time, before Jesse Lingard tucked in the third to add gloss to the scoreline in the 61st minute.
The win sets up a quarter-final showdown with West Ham United at Old Trafford.
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