Villarreal fashioned the best move of the match and almost took the lead after 59 minutes when Franco flicked Angel Lopez's cross against the post with United keeper Edwin van der Sar beaten.
He cut inside defender Stirling but his touch then failed him and allowed Miguel Angel Llera to slide in and tackle with MK Dons keeper Willy Gueret gathering the loose ball.
And Wigan boss Paul Jewell's heart will have been in his mouth as Angel's shot bounced just in front of Filan and the keeper was fortunate to see it hit his hands and loop just over the bar.