The Frenchman was set to have tests to assess the problem at the Gunners' London Colney training ground on Thursday.
Flamini was the main casualty of the 2-0 win, which was the first time this season that Arsene Wenger had significantly rotated his squad for a Premier League match.
Of the five changes made from the Saturday's win over Cardiff City, the only two that were enforced were Bacary Sagna (hamstring) and Olivier Giroud.
In relation to the latter, the France international has an ongoing knee problem, so the midweek fixture with Hull was seen as an opportune time to give him a break.
Wenger had also intended to rest Mesut Ozil but the coach felt that his side could not do without both the Germany international and Giroud, given both have contributed significantly to Arsenal's fine form this season.
Theo Walcott had been primed to make his first start since Sept. 18 but ended up being a substitute for the third consecutive match after struggling with an illness in the build-up to the game.
The Gunners are preparing for a testing six-day period in which they play Everton at home before trips to Napoli and Manchester City.