Manager Mickey Callaway said after the game that Flores would fly back to New York to be checked by a doctor.
"I'm sure you guys have seen him having a tough time throwing the ball. He feels like he can't really bend over,'' Callaway said.
The Mets are traveling from Milwaukee to Atlanta for a Monday day-night doubleheader, and they will have a minor league player on standby to join them in case Flores has to go on the disabled list.
Information from The Associated Press was used in this report.