Al Habsi battled through the 90 minutes despite the problem as Wigan fell to a 2-1 defeat at the DW Stadium but now the club fear that he may have a trapped nerve in his shoulder.
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"Ali picked up a little knock in his shoulder and we were concerned before the game," the Wigan boss told reporters. "He was able to play, and now we can assess his situation."
The 30-year-old was set to start for the Oman national team in their crucial World Cup 2014 qualifier against Japan on Wednesday.
Oman have made the fourth qualifying stage and sit third in Group B, behind Australia only on goal difference, despite being the second lowest seed of the 10 teams that remain in contention in Asia.
Al Habsi has started all of Wigan's Premier League matches this season and was named the club's player of the year in 2011.