The energy interruption of the main line on the east coast causes major disruptions in the network.
The National Railways said the offer failed at 17:37 GMT between Newark North Gate and Retford, which affected the trains that traveled between Peterborough and Doncaster.
Railways said employees were trying to fix the mistake and save the trains that had become trapped.
Many services, including up to and from London, were canceled on Wednesday night due to ongoing disruptions.
The London-based Northeast Rail Railway apologized for the delays and advised travelers not to try to travel on Wednesday, unless absolutely necessary.
Tickets for Wednesday will be valid for Thursday, or customers will be able to apply for a full refund for unused tickets, the firm said.
The national railways advised travelers to check their trips before the trip.
A spokesman said the engineers were in place and that "they would work hard at night to restore full passenger service" on Thursday.
"We understand the inconveniences this incident caused to customers and apologized for the interruption of their journeys."
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