The travellers who were offered “free” replacement flights discovered they were not refunded for charges on extras paid on their original booking, leaving them having to pay twice.
The Dublin-based carrier - which is shelving up to 50 flights daily over the next six weeks - said it is aware of the issue and any customers who were double charged for seats or hold luggage will be refunded.
One passenger told the Daily Telegraph that the website would not let them book on a flight “unless I paid twice for the seats and bags”.
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Consumer rights group Which? said it was “outrageous” that people could be double charged and urged the airline to issue refunds swiftly.
Alex Neill, managing director of home products and services, said: “It’s outrageous that Ryanair passengers who have had already to endure huge inconvenience are essentially being double charged for booking seating and luggage.
“The airline must quickly ensure affected passengers are re-booked, fully refunded and automatically compensated without having to jump through hoops.”
Kenny Jacobs, the airline’s chief marketing officer, told the Telegraph: “We are aware of this issue and any customer who has been double charged for bags or allocated seating will be refunded.”
Ryanair faces a compensation bill of up to 20 million euro (£17.7 million) over the cancellations brought about by the over-allocation of pilots’ holidays during a relatively busy period.
The airline said it was cancelling flights at airports where it ran the busiest schedules so it would be easier to place passengers on alternative flights.
Customers affected by cancellations which run until October 28 will be emailed offers of alternatives or full refunds and details of their compensation entitlement, the budget airline confirmed.
Michael O’Leary, the airline’s chief executive, told a press conference on Tuesday that it was clear the debacle had a “large reputational impact” and apologised.
A Ryanair Spokesman said: ““We have resolved this issue, which only affected a small number of customers, and anyone who has been charged twice will be refunded.”