The Edmonton native finished eighth in the day's third and final event, the elimination race, dropping her to fourth overall with 18 points.
Britain’s Laura Trott and American Sarah Hammer were tied on 12 points at the top, followed by Annette Edmonson of Australia with 17.
Omnium features six events spread over two days and awards the gold to the athlete with the lowest points.
Whitten hung on the front of the elimination race for most of the first 30 laps, staying out of the last, and eliminated, spot each time a two-lap sprint was signaled by the bell.
But on sprint 10, the Canadian found herself shoved back in the pack where it looked as though she might still be safe until a rub against the back wheel of an opponent cut her momentum and Whitten went out.
Unfortunately, her three main competitors for medals stayed in to the end with first Edmunson dropping, and then Trott beating Hammer to the final line.
Trott earned just one point, Hammer two and Edmundson three, moving them up the standings. Whitten's eighth was for eight points.
Whitten turned in a strong performance in the earlier points race on Monday afternoon to move into second overall at that time.
She scored a 28 in the second of six events, picking up 20 lap points and eight total for the sprint, good for third in the race behind Malgorzata Wojtyra of Poland and Tatsiana Sharakova, of Belarus.
American Sarah Hammer was fifth, to move into first overall at that time.
Whitten was seventh after the first timed sprint race, clocking 14.516 seconds in the 250-metre flying lap time trial. Trott led the field of riders by cycling to a 14.057 result. France's Clara Sanchez (14.058) and Edmondson (14.261) rounded out the top three.
Women's omnium will finish Tuesday with the 3-kilometre individual pursuit, 10km scratch race and the 500m time trial.