The confusion was made possible because the finish line was parallel to where the riders went, with just barriers separating the right and wrong track.
Some of the riders who took the wrong turn were forced to lift their bikes over the barriers to cross the finish line.
But his victory was later stripped away as race commissaires cancelled the stage and declared no winner, denying Ratcliffe and Ineos a win.
Ganna was one of a handful of riders who chose the correct route and he was able to power across the line first.
Filippo Ganna crossed the line in first place for Ineos before the stage was cancelled.