They were told that it was closed even though they said they arrived at 11pm for their flight which took off at 1.45am on Thursday.
Those who made it back before 4am yesterday have avoided forking out £1,750 for eleven nights of hotel quarantine.
More than 20 flights have been chartered to return to the UK from Islamabad, Karachi and Lahore in the past 24 hours, according to reports.
According to a recent BBC North West Tonight report, around 32,000 travellers flew from the UK to Pakistan in January alone.
With thousands more still in Pakistan, Labour MP for Bolton South East Yasmin Qureshi called on Boris Johnson to lay on more chartered flights for stranded citizens.
A letter to the PM signed by 46 MPs and co-authored by Qureshi said that the country currently has a lower infection rate than the UK and asked for clarity over the Government’s reason for placing it on the list.
Her intervention came after reports that thousands of British Pakistanis were stuck in the country, many of whom flew there legally under the Government’s travel guidelines.
The letter read: “The vast majority would have travelled to visit family, including elderly relatives, whom they have not seen for over a year.
“They would already have paid for return flights but are now in a position where they will have to pay for new flights in order to return before the ban is put in place.”
British Airways, Virgin Atlantic, Pakistan International Airlines and Polish carrier Enter Air have arranged extra direct flights in recent days.
According to data from the website FlightRadar24, five flights were scheduled to land in England direct from the Pakistani capital Islamabad yesterday.
Some of the last-minute seats were going for more than £1,400.
