Fans in the Leppings Lane end removed netting from seats to try to prevent crushing around the tunnel that leads to the lower tier.
The same stand was the scene of the Hillsborough tragedy in 1989, which resulted in the deaths of 97 Liverpool fans after a crush.
Some Newcastle fans have suggested overcrowding happened when supporters came through a tunnel to the central pen. Fans also voiced their concern at what they said was a lack of stewards on duty.
The FA will speak to officials from both clubs, while safety officers will be asked for their thoughts.
The Newcastle United Supporters Trust have appealed for information and asked the 4,500 travelling fans to share their experiences. One told The Times: “There was an area cordoned off with nets. We had to pull it off to make a space because there was nowhere to go.”
League One side Wednesday caused a third-round upset as they beat Newcastle 2-1.