Assistant referee Mark Scholes was the target from some of the home supporters, who appeared to launch bottles at him after a foul was awarded against Millwall.
Referee Neil Swarbrick temporarily stopped play in response to the actions in the second half, with John Marquis later grabbing a headed winner in the 89th minute, which saw the Premier League side crash out.
Three people have been arrested so far and the Football Association are also set to take matters in their hands, with a spokesman confirming that: "We will be looking into it. We are awaiting the referee's report plus details from an FA crowd advisor who was present."
Millwall manager Kenny Jackett has responded to the incident by stating that there is no room for actions of that manner in the stands.
"We can't condone people throwing bottles on to the pitch. That doesn't help us," he told reporters.
"There's a line between supporting your club and creating a passionate atmosphere but we don't want to step over that line."