Southern train services continued to be disrupted on Thursday, even though drivers returned to work after a 48-hour strike.
An overtime ban by Aslef in the bitter dispute over driver-only trains was still in place, causing more misery for passengers.
A statement on Southern's website said: "Services across our network continue to be subject to possible short-notice disruption with no service at all on some of our routes and a reduced service on others. Please check your journey before travel."
Another strike will be held on Friday and again for three days later in the month.
Southern warned there will be no services on Friday because of the strike.
Commuters who changed to neighbouring Southeastern services, which are not affected by the dispute, were hit by major delays into London Charing Cross caused by a signalling problem.
Southern's owner, Govia Thameslink Railway, is taking fresh legal action against the Aslef union by going to the Supreme Court to try to stop the strikes.
GTR lost a court case and an appeal last year.
A statement said: "GTR is determined to protect its passengers and its business from unlawful industrial action.
"GTR is therefore prepared to continue its legal claim to the Supreme Court, as it believes that it has an arguable case that the industrial action is unlawful under EU law."
Last month, the High Court rejected an argument from GTR that industrial action would breach customers' rights.
Aslef described last month's legal action as a waste of taxpayers', shareholders' and passengers' money.