Nottingham Forest are taking on Huddersfield Town at Wembley, with the game due to kick off at 4.30pm.
One fan, Andy, told the PA news agency: “We were supposed to be in first class on a 10 carriage train.
“There were only five carriages.
“It was like a packed Tube train at rush hour.”
Another fan told PA: “I would say EMR massively underestimated numbers of Forest fans going by train, but to be fair to them they brought later trains forward with more carriages.
“If however you were waiting for later trains, queues were on to London Road.
“It’s going to be mad going back again.”
Thousands of Forest fans are expected to make the journey to London.
EMR has since relaxed its ticket restrictions to enable customers with booked tickets to travel on any service.