Shortly after providing the cross for Matt Smith to open the scoring in Sunday's famous 3-2 triumph, M'Changama sustained a knee injury from a challenge that earned Reds winger Raheem Sterling a booking.
Although scans showed no cartilage or cruciate ligament damage for the 22-year-old left-sided midfielder, he has suffered a snapped medial ligament.
"There's a good chance it could be the season, unfortunately," Latics boss Paul Dickov confirmed.
"He's snapped his medial ligament, which is unfortunate because the kid was coming into a bit of form as well."
Two-goal hero Smith picked up a shoulder injury during the closing stages, while strike partner Robbie Simpson also failed to complete the 90 minutes due to a hamstring tear.
Dickov added: "We're light on numbers anyway and it looks as if Robbie and Matt are going a few weeks as well.
"Robbie's got a slight tear on his hamstring, Matt's torn some cartilage in his shoulder."