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
Showers often confined to northwest Scotland - filtering further south at times.
A Spanish court has released photos of four suspects they are hunting over the terror attacks in Spain.
Wet and windy for a time across many areas through this evening