It is, officially, Britain’s most overcrowded train: the 4.22am service from Glasgow to Manchester, which regularly arrived at its destination carrying more than double its passenger capacity.

But in a week when commuters expressed anger at yet another rail fares increase, the Guardian found the service to be eerily quiet. Everyone found a seat as the four-carriage train trundled out of Preston on Friday morning.

Where were the crowds? It transpires that months after it topped the overcrowding league for autumn 2017, Transpennine Express axed a stop at Wigan, in the busiest part of its route, meaning passenger numbers plummeted overnight.

Cutting out Wigan shaved 10 minutes off the journey time, the company said on Friday. It also means the service will almost certainly no longer come out worst when new figures are published in July. As for Wiganers, Transpennine said they were able to catch a Northern Rail train instead.

“I moved up from London in April, so I’m used to being packed in like sardines, but at least it used to turn up,” said Yas Patel, 31, who found a seat outside the train toilets for the 40-minute journey from Preston to Manchester. In the last nine months, he said, delayed trains had made him late for work on all but 30 occasions.

National Rail statistics show that his Preston-Manchester service has been on time only five times since October. The return leg, leaving at 6.26pm, has been late every day. Transpennine said its industry-recognised target was for trains to be less than 10 minutes late.

“It’s a shame. For the price, you would expect a better service,” said Patel, an account manager, who pays £73.10 for a weekly train pass, compared with the £40 he used to pay to get around London. “You’d think it would be cheaper than London. It’s cheeky considering what was going on last year with the delays.”

Facebook Twitter Pinterest Yas Patel: ‘I’m used to being packed in like sardines.’ Photograph: Christopher Thomond/The Guardian

Many passengers are at their wits’ end. It emerged this week that overcrowding on trains is at its highest level in years and the number of cancelled or significantly late services has reached a 17-year high. A study of government figures by Labour found the most overcrowded services were on average running at 187% of capacity in 2017, an increase of 25% since 2011.

The above-inflation fare rise of 3.1% adds insult to injury. “You try to leave Manchester between 4pm and 6pm and every train through to Preston is just absolutely packed, you very rarely get a seat,” said Stuart, 33, who did not wish to give his surname.

The price of his annual ticket from Preston to Stockport had just risen to nearly £4,000, making it almost as expensive as buying his own car. “The fact is, trains are a public service,” he said. “It shouldn’t be comparable to having your own vehicle.”

There are also increasing safety fears. Network Rail security officers patrol Manchester Piccadilly’s two notoriously busy platforms, 13 and 14, ordering crowds to keep back to prevent a crush as trains approach. Northern Rail strikes have made the situation worse on Saturdays, as desperate passengers rush for the last train at 5pm.

One commuter who did not wish to be named said she had recently witnessed people “literally trying to hang on to the train while the doors were shutting” on a busy late train from Piccadilly. “There were people pushing each other towards the platform edge, lots of people arguing with each other. It was very dangerous,” she said.

Transpennine Express said: “We recognise that our services, particularly at peak times, can be very busy and we understand our customers’ frustration. That is why we will be introducing extra capacity on our Anglo-Scottish route later this year when our Nova 2 trains come into service, as part of over £500m-worth of investment we are committed to delivering across our network in the next two years.”