The passengers were due to travel from the British Overseas Territory to Gatwick Airport on Monday night, but their flight could not depart until Tuesday due to "low visibility weather conditions".
The airline was unable to book enough hotels rooms in Gibraltar for all the passengers, so some were offered accommodation on the other side of the Spanish border.
Travellers returning to the UK from Spain must self-isolate for 14 days due to the coronavirus pandemic, while those arriving from Gibraltar are exempt.
Passenger Alan Orme sent a message to the airline on Twitter describing the situation as "ridiculous".
He said: "Flight from Gibraltar has been moved to (Tuesday) due to low visibility on a perfectly clear rock.
"My option is to move from low Covid Gibraltar to high Covid Spain. I cannot afford to self isolate. @easyJet will you pay my loss of earnings?"
EasyJet said in a statement: "As a result of low visibility weather conditions in Gibraltar, easyJet had to delay flight EZY8906 to Gatwick overnight.
"The safety and wellbeing of our customers and crew is our highest priority and we would never operate a flight unless it is safe to do so."
The company explained: "We tried to provide as many hotel rooms in Gibraltar as possible however, due to a shortage of rooms it was not possible to provide these for all customers so we offered accommodation in Spain for those who wanted it.
"Some customers found accommodation themselves in Gibraltar and easyJet will reimburse the cost to them.
Easyjet resumes it's flight during Coronavirus lockdown ease
"Whilst the delay was outside of our control, we would like to apologise to customers for the inconvenience caused as a result of the weather."
It comes as the Czech Republic and Switzerland are set to be added to the UK's "red list", meaning travellers must self-isolate for 14 days when returning home.
A seven-day rate of 20 Covid-19 cases per 100,000 people is the threshold above which the UK Government considers triggering quarantine conditions.
The Czech Republic is currently recording a seven-day rate of 19.4 cases per 100,000, up from 16 a week ago.
Meanwhile, Switzerland is also over the threshold, with a seven-day rate of 21.2.
Last week, Scotland took Switzerland off its list of countries from which people do not need to self-isolate on arrival, and the rest of the UK could follow later this week.
Paul Charles, chief executive of travel consultancy The PC Agency, said Switzerland is "sadly likely to be added" to the list of countries from which people must self-isolate for 14 days.
"It’s been above the Government’s own criteria for several days now," he said.
"The Czech Republic and Jamaica are both going to be closely watched and potentially added.
"At bank holiday time lots more Britons travel and Prague is a popular weekend break destination so if they’re added to the list it will affect several thousand people."