Merseyrail has apologised after passengers claimed they were hours late to work and crammed on platform and trains.
People travelling on Wirral lines on Thursday said they faced long delays in both the morning and evening.
One passenger who regularly used the Liverpool to West Kirby line said the situation was not helped as there were only three-cars on the train.
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They said: "There are only two trains an hour at peak times.
"One has two three-car sets on it, but there's another one with only three-cars that seems to turn up at random.
"The one I was on had only three cars, at rush hour, and it was absolutely packed. People were crammed in cheek by jowl.
"At Conway Park a disabled lady in an electric wheelchair was unable to get on because it was so busy. So if the trains are only one every half an hour, she might well have ended up waiting there for another half an hour in the cold and wet. It's unacceptable.
"And from a covid perspective it's horrendous. People crammed into each other's personal space everywhere you looked. They might as well call it the Covid Express."
Posting on Twitter, many people said they were late to work and trains were forced to stop at stations for long periods of time.
In reply to Merseyrail, one person said on Thursday: "Which one? This morning's incident which made me two hours late for work or this evening's one which has made my journey home take an hour longer? Not good enough.
Another person added: "Signal problems at Birkenhead this morning, I was 40 minutes late for work this morning and now my girlfriend has to drive over to pick me up because I now can’t get home."
A third person on Twitter also said: "45 mins we’ve been stood at Birkenhead North. Shambles."
One woman also asked whether the train service was back to normal, she said: "Are the trains from Hooton running as normal today? After yesterday I don’t want my daughter having a dreadful journey again."
A photo shared on social media on Thursday night showed passengers crammed on James Street platform for Wirral lines after the delays.
Earlier this week Merseyrail confirmed it will be increasing its rail services from Monday, February 14.
Changes to the timetable include services increasing to 20 minutes on the Southport & Hunts Cross and Ormskirk & Kirkby lines, Monday to Saturday until 8pm. A 30-minute services will remain in place on both lines every Sunday.
The Chester Line will return to a 15-minute frequency from 7am until 7pm. They will operate every 30 minutes before and after these times.
The Ellesmere Port line will continue to operate a 30-minute service all day. A 30-minute service will also remain in operation on Sundays on both lines.
West Kirby & New Brighton services will continue to run every 20 minutes from the start of service until 7pm. They will then operate every 30 minutes until the end of service. A 30-minute service will continue to operate on Sundays.
Since the hold-ups, commercial director for Merseyrail Suzanne Grant said the reasons for the disruption on Thursday morning was caused by a "damaged cable" which had to be repaired.
In the evening, the disruption to train services was due to "emergency work" being carried out on one of the platforms at James Street station.
Merseyrail has since apologised to passengers who were travelling on the Wirral lines for the inconvenience.
Ms Grant said: "Passengers travelling on our Wirral lines may have experienced some disruption to their journeys on Thursday, February 3.
"Disruption during the morning was caused by a damaged cable that had to be repaired.
"Disruption in the evening was due to emergency work having to be carried out on one of the platforms at James Street station.
"On behalf of Merseyrail, I would like to apologise to you for the inconvenience caused if your journey was disrupted."
