I wasn't aware of the players' situation at the time I created the team, just that they were a Japanese team so that's what flag was given to the team. It was a rather low priority earlier to go back and change that.
I believe the flag on the match page didn't automatically update to BR because the players don't have profiles yet with flags set, so it fell back to the flag set for the team. (we don't create player profiles until after their first match has been played).
Although it isn't quite the same as other teams, such as MIBR since the players of this team are all dual nationals and they are for all intents and purposes a Japanese team, so if they wanted they could choose the JP flag to represent, but in this case they opted for the BR flag.