The Manchester United right-back came on as a first half substitute for Diogo Dalot after the Portugal international went off injured at Old Trafford.
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And the visiting Addicks supporters jeered Wan-Bissaka in unison, with the 25-year-old a former player at their south London rivals Palace.
talkSPORT's Adrian Durham was loving the pantomime banter at the Theatre of Dreams, where United ran out 3-0 winners.
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But he was quick to remind the League One outfit that one of their star players is currently on loan from Patrick Vieira's side.
Speaking at half-time, Durham said: "I love the fact that the Charlton fans are booing Wan-Bissaka because he's from Palace.
"But what about [Jesurun] Rak-Sakyi? He's on loan from Palace!
"Why aren't they booing him?"
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Rak-Sakyi has been a key player for Charlton this season, with the 20-year-old chipping in with six goals in 22 League One games.
Charlton went into the break 1-0 down in their quarter-final clash following Antony's stunning strike from distance in the 21st minute.
The Brazilian winger picked up the ball down the right flank, where he cut onto his left foot and curled a shot home into the bottom left corner from 25 yards out.
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Marcus Rashford came off the bench to put the tie to bed, where he scored twice at the death to find the back of the net in six straight games.