As I said above, its commonplace (or used to be), while films often comprise at least some footage that isn't necessarily used/edited in anything like the same order it was filmed, or sometimes not from the same place, the same time or even by the same people/company! As shown by this, even the BBC with its high standards and massive production budgets can't avoid doing this occassionally- its the name of the game.
But nobody is normally any the wiser with the finished product. Only a situation like this where the press have flagged it up does it become an issue.