The German defender landed awkwardly on his ankle after a collision with Gunners goalkeeper Emiliano Martinez.
"I hope I'm wrong but when a central defender is taken off on a stretcher it is not usually good," Arteta said.
"We will find out more in the next days and we will assess it."
The Gunners already have problems in defence with Calum Chambers, Kieran Tierney and Sead Kolasinac all out injured.
Brazil defender David Luiz was also absent from their win on the south coast through suspension but will be available for their trip to Burnley in the Premier League on Sunday.
Mustafi, 27, has started Arsenal's past three matches. He was replaced by Rob Holding in an area of the pitch that Arteta has already determined needs reinforcement.
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