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
Four QPR hooligans caught on CCTV reeking havoc and attacking rival fans have been jailed.
Ex CPS boss says it was a "serious failing" by prosecutors not informing him of an investigation into allegations against Lord Janner.
Today there'll be plenty of sunshine across the British Isles with wispy cloud towards the coast.