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'."
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Rescue workers are at the site Sunday morning trying to cut open mangled coaches.
Despite chilly temperatures it will be a mostly dry day, and milder than yesterday.
The Sunday Times alleges a missile malfunctioned after launch during a routine test of the UK's nuclear deterrent last year.