The native of Whitehorse faded in the third stage of the grueling competition and will head into Sunday's events in ninth place overall with 30 points — 20 behind the leader.
After a strong start in the first leg — the flying lap 250-metre time trial earlier in the day in which he placed seventh — he struggled in the 30-kilometre points race and wound up 13th in the stage.
France's Bryan Coquard currently leads the overall competition (10 total points) after placing first in the elimination race, while Italy's Elia Viviani (13) is in second place and Australian Glenn O'Shea is in third and nipping at his heels with 14 points.
Eighteen riders start the elimination race with the last-place rider getting eliminated every two laps.
In the omnium, competitors are awarded the same amount of points as the spot they finished in with the goal being to accumulate the least amount of total points.
The competition continues with the four-kilometre individual pursuit Sunday, followed by the 15-km scratch race and one-km time trial.