Staff shortages, signalling problems, a landslip and ongoing industrial action were among the issues affecting the network on Monday morning.
Industry body the Rail Delivery Group (RDG) insisted the problems were "unrelated" and the "vast majority of services are running as planned".
Passengers travelling with Transpennine Express - which operates across the North of England and into Scotland - appeared to suffer the worst disruption.
Rail data website trains.im stated at 9am that 47 per cent of the firm's services were either cancelled or at least half an hour late.
Affected routes included those linking Manchester Airport with Edinburgh and Newcastle, and trains from Liverpool Lime Street to Scarborough.
Managing director Leo Goodwin said: "I am really sorry for the disruption to our customers journeys. I know what a busy time it is whether people are trying to get to work, trying to get home to see school plays, visiting loved ones or trying to go out and enjoy their Christmas parties.
“Due to a number of issues with crew training caused by the late delivery of some of our new trains, along with a maintenance backlog and some infrastructure issues we have had to implement a temporary timetable, cancelling some journeys along one of our routes. This has unfortunately made a number of other services a lot busier. We are working really hard to sort this for our customers and as we introduce more new trains we should see an improvement to people’s journeys.”
One passenger, posting a message to TPE on Twitter with the username @leylandski, wrote: "Every day you get worse. Now you've cancelled both my train to and from work until Jan? Why? They were during peak time, this is totally unacceptable."
Some early-morning services operated by Northern were cancelled due to a shortage of drivers.
The operator's website listed the issue as affecting a number of services, including between Blackpool North and Manchester Airport, Leeds to York and Sheffield, and Darlington to Saltburn.
Despite this, the company stated the new timetable had performed well.
A Northern spokesman said: "“The new timetable for Northern has performed well.
"The small number of delays and cancellations are due to operational issues including crew sickness, signalling and train faults.”
RDG director of nations and regions Robert Nisbet said more services are now running than before the timetable change and that passengers will benefit from 1000 more services a week.
Anthony Smith, chief executive of watchdog Transport Focus said commuters want things running again as soon as possible.
Mr Smith said: "Passengers don't care what causes the disruption - they just want things running again as soon as possible, and plenty of visible staff on hand to help them in the meantime.
"Train operators should ensure every eligible passenger knows how to claim compensation so that they get the money they are entitled to."
Train timetables are changed twice a year, in May and December.
The infamous botched change of May 2018 led to chaos, and passenger watchdog Transport Focus said travellers would be hoping for a smoother introduction with the latest changes.
What happened in May 2018?
The introduction of new timetables in May 2018 led to thousands of cancelled or delayed trains with Northern forced to introduce an interim timetable with reduced service levels in order to keep the trains moving.
A staggering 43 per cent of the operator's trains across the North failed to arrive on time and nearly 500 trains were cancelled or very late.
Beleaguered Transport Secretary Chris Grayling told a Commons debate at the time that Network Rail was responsible due to its failure to deliver engineering upgrades in time.
A document circulated by the agency, which is responsible for the nation’s rail infrastructure and co-ordinating the timetables supplied by operators, acknowledged that the failure to complete an electrification project between Manchester and Bolton in January of that year “meant the whole of the new timetable for the North would need to be re-written”. It blamed “unforeseen poor ground conditions hampering progress” for the delays, but added that “matters were “compounded further” by the collapse of outsourcing giant Carillion and cited other changes around the country that hampered its work.