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A rail firm cancelled dozens of trains - hours after its new timetable began.
Govia Thameslink Railway (GTR) rescheduled every service on its Great Northern, Thameslink and Southern franchise as part of an overhaul billed as the biggest in the UK.
It said the "huge logistical challenge" of introducing the new timetable meant "some services are not initially running".
It was unable to confirm how many trains had been cancelled on Sunday.
A GTR spokesman added: "We are working hard to minimise the impact this will have on our busiest trains. This situation will improve."
The Thameslink, Southern and Great Northern rail franchise includes services to Bedford, Luton, Peterborough, King's Lynn, Cambridge, London King's Cross, London Moorgate, Wimbledon and Brighton.
No entire routes were cancelled on Sunday but "occasional trains" were not running, said a spokesman.
'Any clue?'
The company announced on Twitter "a short-term amended timetable" was in place across the network, with disruption expected throughout Sunday.
Frustrated passengers tweeted to complain about the disruption, with one asking "Any clue as to the reason? No drivers by any chance? Or explain the operational incident please."
The company replied: "Unfortunately we are not privy to this information".
From Sunday, every schedule for Thameslink, Southern, Gatwick Express and Great Northern trains has been changed, in an attempt to improve rail efficiency in the South East.
It will mean 400 extra trains a day and new direct services from 80 stations into central London.
But passengers in a number of smaller locations complain they will be served with fewer or slower services.
And the RMT union claims passengers with reduced mobility may be left behind if a train is at risk of delay.
GTR said it placed high priority on making its services accessible to all.