One passenger told the BBC she waited for two hours at passport control, another said after a flight from Cork she waited so long they were put into another area.
Other passengers expressed their frustration on Twitter.
Sophie Elliot posted on the social networking site: "Last night at Stansted we were trapped in queues of over an hour - longer for the people behind us - cos 'a few planes landed early'."
More top news
It will be hotting up as we approach the weekend as we draw in very warm air from the Continent - it'll feel more like summer than spring.
A new scam aimed at people who own Apple iPhones steals their account information through a text.
Tomorrow’s Congress is expected to be dominated by claims of North Korea’s nuclear prowess.