As MLB.com's Austin Laymance notes, Puig wasn't injured, and the Dodgers were already working with a short bench. The working assumption, at the time, was that it was a disciplinary move on the part of Mattingly.
On that front, more from Laymance:
Puig made a pair of nonchalant catches in the outfield in the top of the fourth inning and did not return for the fifth. He also did not slide into second base in the first inning on Carl Crawford's double-play grounder.
Sure enough, we found this out after the game from Puig himself:
Puig said Mattingly pulled him because he wasn't ready on defense for every pitch. Puig said he understood Mattingly's decision.— Dylan Hernandez (@dylanohernandez) August 28, 2013
Puig, of course, has been the source of some controversy this season, what with his bravado, somewhat hyperactive style of play and occasional deviation from the fundamentals. On the other hand, Puig is batting .346/.406/.557 in 2013. The challenge for Mattingly, then, has been balancing "teachable moments" with the broader interests of a contending team.