I see it all the time. It is my bugbear
E is more popular
It is used more in our language.
One of the main things the mind does is create a narrative. Time is usually what structures the events in a story: 'Once upon a time, Jack went there, then there, then over to England, then back to Boston.'
'Stream of consciousness,' itself can be understood as ourselves noting this then that then that...
It would then follow that since people use 'then' more than 'than,' that 'then' would then be the most misused (in place of 'than').