The Janeway Factor was an informal term used by Captain Braxton with regards to Captain Kathryn Janeway of USS Voyager. Braxton considered Janeway's meddling with the timeline a major annoyance, and coined the term to describe it. (VOY: "Relativity")
One of the occasions he listed included when Voyager traveled back to 1996 to stop Henry Starling, and then left Braxton on 20th century Earth. (VOY: "Future's End", "Future's End, Part II")
Braxton's remark could have referred to any of these incidents.