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Fulham complained that Manuel Akanji, stood in an offside position, had attempted to kick the ball on its way past and hindered Bernd Leno.
In the previous encounter against City last November, Fulham narrowly lost due to a 90th-minute penalty from Erling Haaland.
Julian Alvarez and Nathan Ake were also on target.
A late Bryan Mbeumo goal earned Brentford a home draw against Bournemouth.
Fulham ended up losing 5-1 after Nathan Ake’s header on the stroke of half-time was allowed to stand.