The judge told the Daily Mail that he stands by his preference for the latter dance troupe after watching the repeats of last Saturday's final.
Morgan said: "I think Flawless were unlucky to have gone on first. If they had gone last it may have been different.
"They're both amazing dance groups. Diversity were just very lucky."
The presenter has previously suggested that the publicity surrounding Susan Boyle put people off voting for her to win the show.