Several passengers took to social media to express their frustration, claiming the crew would have known the plane would not arrive before curfew and should not have departed.
Irish traveller Barry Masterson said some people took a while to realise they were not in Portugal.
"Got on a @Ryanair flight to Faro and I'm in Malaga lads, you couldn't make this up," he wrote.
"Morale is low, some people are only just realising we're in Spain."
Masterton kept followers updated throughout the journey and claimed he had to spend an additional €55 ($93) on a taxi for the last leg of the journey.
He suggested Ryanair knew they would not arrive on time after a long delay.
"Our best assumption is that Ryanair knew we could never land in Faro because our flight was delayed so long the airport would be closed before we made it. So they lied and flew us to Spain so they wouldn't have to refund everyone," he wrote.
Aileen Marron, who was also on the flight, agreed.
"Disgraceful service by Ryanair, who never had any intention of taking us to Faro, we know now the airport closed at 2am, we took off just before 1am Portugal time," she wrote.
As Masterton's original tweet gained attention, people pointed out that the plane should have landed in Seville instead of Malaga, as it is much closer to Faro.
A Ryanair spokesperson apologised to passengers and blamed a French Air Traffic Control (ATC) strike. They claimed the strike had affected the departure time, which meant they did not depart on time or reach Faro before curfew.
"This flight from Dublin to Faro diverted to Malaga having missed Faro Airport's curfew due to disruption from the French Air Traffic Control (ATC) strike, which was entirely beyond our control and impacted all airlines flying to/from/over France that day," they said.
"To minimise disruption to passengers, Ryanair quickly arranged for a coach to transport passengers from Malaga Airport to their final destination.
"Ryanair sincerely apologises to passengers for the inconvenience caused as a result of this unjustified French ATC strike."
Hundreds of flights were disrupted as a result of the one-day ATC strike on September 16. Almost half of the flights due to arrive or depart from Paris airports or use French airspace were grounded according to Reuters.
The strike was related to demands for more staff and pay hikes.