Figueroa had to leave the field after only 28 minutes at Turf Moor having sustained the injury, while team-mate Paul Scharner required 10 stitches stitches in a facial wound he picked up creating the Latics' third goal for Emmerson Boyce.
The damage to Scharner is only superficial, but Figueroa's condition is more concerning for manager Roberto Martinez, who told the Wigan Evening Post: "Maynor has a grade two medial ligament problem in his left knee. We will assess it further to see how bad he is, but it doesn't look too good."
He added: "Normally with this sort of injury, you are talking about weeks rather than months - but the signs are not nice.
"He actually wanted to carry on, but the injury was serious and he couldn't do so.
"It's not an injury that he would have damaged any further as it was just a tear - it's muscle problems that can get worse - but Maynor felt so uncomfortable that he had to come off."
Scharner only played on Saturday after passing a late fitness test on a hip problem, while Chris Kirkland also put his hand up for duty despite a painful finger injury.
Martinez continued: "Paul and Chris both played through the pain barrier, while Hendry Thomas took a nasty knock in the face from the ball in the second half which affected his vision.
"It shows you the character that is in the squad and, when you have that attitude - when your team will do anything to win a game - it's something to be proud of.
"Paul battled on to make a difference and now has 10 stitches above his eye to worry about, but there were no reactions to any of the existing injuries."