A spokesman for Southern Railway said the delays at London Bridge were caused when a train was signalled into the wrong platform at the station.
The 10-carriage train arrived at a platform intended for trains with eight carriages.
The spokesman said: "It meant the train had to be sent back along the track, which caused congestion."
Passengers faced delays of about 20 minutes before services returned to normal at 8.30am.
One of the main Tube lines serving the Olympic Park was suspended as hundreds of thousands of people made their way to Olympic events
Tube trains to the Olympic Park suspended because of fire alert
PM on Olympic Transport