Cespedes will have an MRI on Friday, and manager Terry Collins called the injury "a concern."
Cespedes was replaced in the top of the sixth inning of the Mets' 6-4 loss to the Phillies. The left fielder walked in the fifth, was forced out in a double play and was finished for the night.
Cespedes began the game hitting .255 with six home runs and 10 RBIs.
The Associated Press contributed to this report.