Rail users already facing above-inflation fare rises next week, also had to contend with delays to some rush-hour services as they returned to work after the Christmas break.
Prolonged engineering works in the Haymarket area of Edinburgh caused hold-ups in Scotland to services run by five train companies, including East Coast, Virgin West Coast and ScotRail.
Further south, a signalling problem at Teddington in south west London caused delays to South West Trains' services, with no trains able to run between Shepperton and Teddington.
A broken-down train at Imperial Wharf in London meant delays for passengers travelling on services run by the Southern and London Overground companies.
The incident led to a suspension of services between Clapham Junction and Kensington Olympia and alterations on other routes in the area.
Another company to suffer delays this morning was First Great Western, due to a problem with lineside equipment at Greenford in west London, which hit some services in and out of London's Paddington station.
There were no trains between Greenford and West Ealing.
From January 2, regulated rail fares, which include season tickets, will be rising by an average of 6.0%, with some commuters having to fork out even more than this.
An annual season from Bishop's Stortford in Hertfordshire to London, for example, rises 7.09% next week, while a Northampton-London annual season increases 6.92% to £4,756.
Pressure group Railfuture told Press Association that the annual rises were "unfair".
The group's spokesman, Mike Crowhurst, said: "Rail passengers are penalised with increases above inflation every year. I don't think motorists or airline passengers will be suffering price hikes like this.
"Even though there have been recent air charges and fuel price rises, allowing for inflation, driving and flying are as cheap as they were 10 years ago."
He went on: "The Government uses the RPI inflation figure instead of the lower CPI for calculating rail fare increases, while pensions and wages are based on the lower CPI figure.
"This is unrealistic and just makes rail travel less and less affordable. Train operators can also make travel more expensive without changing any ticket prices. They can change the definition of 'peak' times so that passengers have to upgrade from a discounted ticket to a full-price one."
The report into rail costs by Sir Roy McNulty has identified efficiency savings in the region of £1 billion.
Mr Crowhurst said: "It's important that any efficiency savings - and there are plenty to be had - are ploughed back into the industry, not swallowed up by the Treasury.
"There's a lot that needs doing - track enhancements, better signalling, electrification, modern rolling stock and enhanced station facilities.
"The Midland main line is crying out for electrification, as is the line to Swansea.
"We know that the Government is trying to reduce the taxpayer's contribution to the running of the railways, which is understandable, but these increases are not necessary because those targets have already been met. Not only that, most of the fare increase goes straight to the Treasury, not the train operating companies."
Mr Crowhurst said rail fares in Britain were "already the highest in Europe" and could drive people on to the roads.
He went on: "You can't cure overcrowding by pricing off demand. There are many reasons why the wider community benefits from a decent rail network, and it's in everyone's interest that passengers are not priced off the railway.
"We need a level playing field. For instance, why is air travel exempt from fuel duty when rail isn't?
"The rail industry pays a huge amount back in tax to the Government - at least £1.4 billion - which only contributes to the high cost of rail fares."