London 2012: Overcrowding at London Bridge station
Commuters were urged to avoid London Bridge, one of the hotspot stations during the Olympics, during the evening rush hour.
The station was overcrowded with long delays for passengers to get to trains after a signal failure at Canon Street rail station.
Southeastern train services were being diverted to London Bridge and Charing Cross.
Transport for London (TfL) said services have now returned to normal.
London Bridge station is one of the main stations taking passengers to see the gymnastics at the North Greenwich Arena.
BBC London's news presenter Victoria Hollins said London Bridge station was "fine for platforms eight to 16, just everything else is a nightmare".
Elsewhere, a key London Underground line to the Olympic Park was suspended due to a fire alert.
People going to Stratford on the Central Line were told services were ending at Liverpool Street due to the alert at Leyton, where a driver reported smelling smoke, thought to be from a locked axle.
To add to the Olympic travel problems, rail services in and out of Liverpool Street main line station were disrupted due to an overhead wire problem between Elsenham and Stansted Mountfitchet in Essex.
This was affecting travellers on services run by the Greater Anglia and CrossCountry train companies.
Elsewhere, services on high-speed trains between St Pancras and the Olympic Park were delayed by 30 minutes due to an incident at Dagenham Dock station.
People had earlier been advised by TfL to use the Javelin service from St Pancras to get to Stratford following the fire alert on the Central Line.
The problems around Liverpool Street came on another busy day for public transport as the first weekday evening football match of the Games takes place at Wembley Stadium.
TfL advised that London was expected to be exceptionally busy throughout the day.
It said people were heeding advice to avoid London if possible and added that while Tube journeys were up 4% on Monday compared to normal commuting days, road journeys in London were down by 20%.
Culture Secretary Jeremy Hunt said London's transport network was coping "extremely well" with the extra demands from the Games.
"The real success of the Games has been that the transport network has coped really well," he added.
"This is a big success story in one of the areas where people were expressing lots of doubts.
"As a city we are coping extremely well."