Castillo went out to his position before the Giants batted in the eighth inning Saturday. Manager Jerry Manuel and a trainer then came out to check on him before the inning started, and Castillo was replaced by Alex Cora.
Castillo singled in the seventh and was stranded at first.
The Mets said Castillo had a bone bruise to his left foot and was day to day. After the New York beat San Francisco 5-4 in 11 innings, Manuel said it's been bothering Castillo for a while and he was removed as a precaution.
Information from The Associated Press contributed to this report.